CPAD 2.0

Entry	PDB ID	Protein Name	Species	Length	Mutation(s)	Class	Type	Method	Resolution (Å)	PMID
S-0091	2BP4	Amyloid-beta A4 protein	Homo sapiens	16	No	Non-amyloid	Inhibitor complex	SOLUTION NMR		16301322
S-0092	2CD0	Immunoglobulin lambda variable 6-57	Homo sapiens	111	No	Amyloid	Protein	X-RAY DIFFRACTION	1.8	10524280
S-0093	2D4D	Beta-2-microglobulin	Homo sapiens	100	L39W/W60F/W95F	Amyloid	Protein	X-RAY DIFFRACTION	2.1	16901902
S-0094	2D4F	Beta-2-microglobulin	Homo sapiens	100	No	Amyloid	Protein	X-RAY DIFFRACTION	1.7	16901902
S-0095	2E8D	Beta-2-microglobulin	Homo sapiens	22	No	Amyloid	Fibril	SOLID-STATE NMR		17108084
S-0096	2F7I	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.6	14711308
S-0097	2F8I	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.54	12820260
S-0098	2F8O	Beta-2-microglobulin	Homo sapiens	100	P32A	Amyloid	Protein	X-RAY DIFFRACTION	1.7	16491088
S-0099	2FBR	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.46	14583036
S-0100	2FLM	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.65	14583036
S-0101	2G3X	Transthyretin	Homo sapiens	127	I84S	Amyloid	Protein	X-RAY DIFFRACTION	1.58	17196219
S-0102	2G3Z	Transthyretin	Homo sapiens	127	I84A	Amyloid	Protein	X-RAY DIFFRACTION	1.9	17196219
S-0103	2G47	amyloid-beta		990 , 40 , 40	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.1	17051221
S-0104	2G48	amylin		990 , 37 , 37	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	2.6	17051221
S-0105	2G4E	Transthyretin	Homo sapiens	127	I84A	Amyloid	Protein	X-RAY DIFFRACTION	2.17	17196219
S-0106	2G4G	Transthyretin	Homo sapiens	127	No	Amyloid	Protein	X-RAY DIFFRACTION	1.85	17196219
S-0107	2G5U	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.8	15610856
S-0108	2G9K	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.85	15610856
S-0109	2GAB	Transthyretin	Homo sapiens	127	No	Non-amyloid	Inhibitor complex	X-RAY DIFFRACTION	1.85	15610856
S-0110	2H4E	Transthyretin	Homo sapiens	127	C10 sulfonated	Non-amyloid	Protein	X-RAY DIFFRACTION	1.45	17175208
S-0111	2HDA	Tyrosine-protein kinase Yes	Homo sapiens	64	No	Amyloid	Protein	X-RAY DIFFRACTION	1.9	17418139
S-0112	2KB8	Islet amyloid polypeptide	Homo sapiens	37	No	Amyloid	Peptide	SOLUTION NMR		19244249
S-0113	2KIB	human islet amyloid polypeptide (hIAPP)		7	No	Amyloid	Fibril	SOLID-STATE NMR		19130518
S-0114	2KJ3	Heterokaryon incompatibility protein s	Podospora anserina	79	No	Amyloid	Fibril	SOLID-STATE NMR		20828131
S-0115	2KJ7	Islet amyloid polypeptide	Rattus norvegicus	38	No	Non-amyloid	Peptide	SOLUTION NMR		19456151
S-0116	2KUN	Major prion protein	Homo sapiens	148	M129/Q212P	Amyloid	Protein	SOLUTION NMR		20661422
S-0117	2L2P	Tyrosine-protein kinase Fyn	Gallus gallus	66	A39V/N53P/V55L	Amyloid	Protein	SOLUTION NMR		22517863
S-0118	2L86	Islet amyloid polypeptide	Homo sapiens	38	No	Amyloid	Peptide	SOLUTION NMR		21723249
S-0119	2LBU	Heterokaryon incompatibility protein s	Podospora anserina	79	No	Amyloid	Fibril	SOLID-STATE NMR		21591034
S-0120	2LFM	Amyloid-beta A4 protein	Homo sapiens	40	No	Amyloid	Peptide	SOLUTION NMR		21726530

Structure

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Sequence & Sec. Str.

Chain 1

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

16

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Zinc-binding domain of Alzheimer's disease amyloid beta-peptide in TFE-water (80-20) solution

the solution structure of the ABeta-(1-16)-Zn(2+) complex in aqueous solution at pH 6.5. The residues His(6), His(13), and His(14) and the Glu(11) carboxylate were identified as ligands that tetrahedrally coordinate the Zn(II) cation. In vitro aging experiments on ABeta-(1-16) led to the formation of truncated and isomerized species. The major isomer generated, ABeta-(1-16)-l-iso-Asp(7), displayed a local conformational change in the His(6)-Ser(8) region but kept a zinc binding propensity via a coordination mode involving l-iso-Asp(7). These results shows the potentiality of the region 1-16 of ABeta to be used as a therapeutic target. The absence of oligomerization upon zinc binding has also been shown.

Literature

PMID:	16301322
Author(s):	Zirah, S., Kozin, S.A., Mazur, A.K., Blond, A., Cheminant, M., Segalas-Milazzo, I., Debey, P., Rebuffat, S.
Reference:	J Biol Chem. 2006 Jan 27;281(4):2151-61. Epub 2005 Nov 21

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Amyloid-beta A4 protein
Alternative Name:
Gene Name:
Sequence Length:	16
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P05067
Keyword(s):	AMYLOID BETA A4 PROTEIN

Structure Information

PDB ID:	2BP4
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:
PDB Classification:	AMYLOID PEPTIDE
Method:	SOLUTION NMR
Resolution (Å):
R free:

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human transthyretin (TTR) complexed with diflunisal analogues- TTR. 2',6'-Difluorobiphenyl-4-carboxylic Acid

Analogues of diflunisal, an FDA-approved nonsteroidal antiinflammatory drug (NSAID), were synthesized and evaluated as inhibitors of transthyretin (TTR) aggregation, including amyloid fibril formation. Biophysical studies reveal that inhibitors dramatically slow tetramer dissociation (the rate-determining step of amyloidogenesis) over a duration of 168 h. This appears to be achieved through ground-state stabilization, which raises the kinetic barrier for tetramer dissociation.

Literature

PMID:	14711308
Author(s):	Adamski-Werner, S.L., Palaninathan, S.K., Sacchettini, J.C., Kelly, J.W.
Reference:	J Med Chem. 2004 Jan 15;47(2):355-74

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2F7I
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.6
R free:	0.252

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
26C	A	C13 H8 F2 O2	234.2	2',6'-DIFLUOROBIPHENYL-4-CARBOXYLIC ACID	c1cc(c(c(c1)F)c2ccc(cc2)C(=O)O)F	CWWIIKLXUPZDOG-UHFFFAOYSA-N
26C	B	C13 H8 F2 O2	234.2	2',6'-DIFLUOROBIPHENYL-4-CARBOXYLIC ACID	c1cc(c(c(c1)F)c2ccc(cc2)C(=O)O)F	CWWIIKLXUPZDOG-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human transthyretin (TTR) complexed with Benzoxazole

Benzoxazoles substituted with a carboxylic acid at C4â€“C7 and a halogenated phenyl ring at C2 complements the TTR thyroxine binding site.

Literature

PMID:	12820260
Author(s):	Razavi, H., Palaninathan, S.K., Powers, E.T., Wiseman, R.L., Purkey, H.E., Mohamedmohaideen, N.N., Deechongkit, S., Chiang, K.P., Dendle, M.T., Sacchettini, J.C., Kelly, J.W.
Reference:	Angew Chem Int Ed Engl. 2003 Jun 23;42(24):2758-61

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2F8I
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 2-mer - A2
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.54
R free:	0.24600000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
205	A	C14 H7 Cl2 N O3	308.12	2-(2,6-DICHLOROPHENYL)-1,3-BENZOXAZOLE-6-CARBOXYLIC ACID	c1cc(c(c(c1)Cl)c2nc3ccc(cc3o2)C(=O)O)Cl	XVNRKPCHMYOPPL-UHFFFAOYSA-N
205	B	C14 H7 Cl2 N O3	308.12	2-(2,6-DICHLOROPHENYL)-1,3-BENZOXAZOLE-6-CARBOXYLIC ACID	c1cc(c(c(c1)Cl)c2nc3ccc(cc3o2)C(=O)O)Cl	XVNRKPCHMYOPPL-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (4 carbon linker)

Monovalent small molecules that bind to one or both of the unoccupied thyroid hormone binding sites at the TTR quaternary structure interface stabilize the native state. Bivalent amyloid inhibitors that bind to both binding sites simultaneously are reported here. The candidate bivalent inhibitors are generally unable to bind to the native TTR tetramer and typically do not engage in monovalent binding owing to a strong inhibitor orientation preference. However, the TTR quaternary structure can assemble around several of the bivalent inhibitors if the inhibitor intercepts the protein before assembly occurs. Some of the wild-type TTR.bivalent inhibitor complexes prepared in this fashion retain a tetrameric structure when subjected to substantial denaturation stresses (8 M urea, 120 h).

Literature

PMID:	14583036
Author(s):	Green, N.S., Palaninathan, S.K., Sacchettini, J.C., Kelly, J.W.
Reference:	J Am Chem Soc. 2003 Nov 5;125(44):13404-14

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2FBR
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.46
R free:	0.22399999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
44C	A	C30 H27 N O6	497.54	4'-(4-{4-[(2-CARBOXYPHENYL)AMINO]PHENOXY}BUTOXY)-1,1'-BIPHENYL-4-CARBOXYLIC ACID	c1ccc(c(c1)C(=O)O)Nc2ccc(cc2)OCCCCOc3ccc(cc3)c4ccc(cc4)C(=O)O	PBSDQYSNDJNJGR-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human transthyretin (TTR) complexed with bivalant amyloid inhibitor (6 carbon linker)

Monovalent small molecules that bind to one or both of the unoccupied thyroid hormone binding sites at the TTR quaternary structure interface stabilize the native state. Bivalent amyloid inhibitors that bind to both binding sites simultaneously are reported here. The candidate bivalent inhibitors are generally unable to bind to the native TTR tetramer and typically do not engage in monovalent binding owing to a strong inhibitor orientation preference. However, the TTR quaternary structure can assemble around several of the bivalent inhibitors if the inhibitor intercepts the protein before assembly occurs. Some of the wild-type TTR.bivalent inhibitor complexes prepared in this fashion retain a tetrameric structure when subjected to substantial denaturation stresses (8 M urea, 120 h).

Literature

PMID:	14583036
Author(s):	Green, N.S., Palaninathan, S.K., Sacchettini, J.C., Kelly, J.W.
Reference:	J Am Chem Soc. 2003 Nov 5;125(44):13404-14

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2FLM
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.65
R free:	0.23399999

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
6CA	A	C32 H31 N O6	525.59	4'-{6-[4-(2-CARBOXYPHENYLAMINO)-PHENOXY]-HEXYLOXY}-BIPHENYL-4-CARBOXYLIC ACID	c1ccc(c(c1)C(=O)O)Nc2ccc(cc2)OCCCCCCOc3ccc(cc3)c4ccc(cc4)C(=O)O	OREPXZDJHRAREJ-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

H

A

G

I

P

M

N

P

A

I

K

R

I

G

N

H

I

25

26

T

K

S

P

E

D

K

R

E

Y

R

G

L

E

L

A

N

G

I

K

V

L

I

S

50

51

D

P

T

D

K

S

A

L

D

V

H

I

G

S

L

S

D

P

N

I

A

75

76

G

L

S

H

F

C

Q

H

M

L

F

L

G

T

K

Y

P

K

E

N

E

Y

S

Q

100

101

F

L

S

E

H

A

G

S

N

A

F

T

S

G

E

H

T

N

Y

F

D

V

S

125

126

H

E

H

L

E

G

A

L

D

R

F

A

Q

F

L

C

P

L

F

D

E

S

C

K

150

151

D

R

E

V

N

A

V

D

S

E

H

E

K

N

V

M

N

D

A

W

R

L

F

Q

L

175

176

E

K

A

T

G

N

P

K

H

P

F

S

K

F

G

T

G

N

K

Y

T

L

E

T

R

200

201

P

N

Q

E

G

I

D

V

R

Q

E

L

K

F

H

S

A

Y

S

N

L

M

225

226

A

V

C

V

L

G

R

E

S

L

D

L

T

N

L

V

K

L

F

S

E

V

E

250

251

N

K

N

V

P

L

P

E

F

P

E

H

P

F

Q

E

H

L

K

Q

L

Y

K

I

275

276

V

P

I

K

D

I

R

N

L

Y

V

T

F

P

I

P

D

L

Q

K

Y

K

S

N

300

301

P

G

H

Y

L

G

H

L

I

G

H

E

G

P

G

S

L

S

E

L

K

S

K

G

325

326

W

V

N

T

L

V

G

Q

K

E

G

A

R

G

F

M

F

I

N

V

D

L

350

351

T

E

G

L

H

V

E

D

I

L

H

M

F

Q

Y

I

Q

K

L

R

A

E

375

376

G

P

Q

E

W

V

F

Q

E

C

K

D

L

N

A

V

A

F

R

F

K

D

K

E

R

400

401

P

R

G

Y

T

S

K

I

A

G

I

L

H

Y

P

L

E

V

L

T

A

E

Y

425

426

L

E

F

R

P

D

L

I

E

M

V

L

D

K

L

R

P

E

N

V

R

V

A

450

451

I

V

S

K

S

F

E

G

K

T

D

R

T

E

W

Y

G

T

Q

Y

K

Q

E

A

475

476

I

P

D

E

V

I

K

W

Q

N

A

D

L

N

G

K

F

K

L

P

T

K

N

E

500

501

F

I

P

T

N

F

E

I

L

P

L

E

K

E

A

T

P

Y

P

A

L

I

K

D

T

525

526

A

M

S

K

L

W

F

K

Q

D

K

F

L

P

K

A

C

L

N

F

E

F

550

551

S

P

F

A

Y

V

D

P

L

H

C

N

M

A

Y

L

Y

L

E

L

K

D

S

L

575

576

N

E

Y

A

Y

A

E

L

A

G

L

S

Y

D

L

Q

N

T

I

Y

G

M

Y

L

600

601

S

V

K

G

Y

N

D

K

Q

P

I

L

K

I

E

K

M

A

T

F

E

I

625

626

D

E

K

R

F

E

I

K

E

A

Y

M

R

S

L

N

F

R

A

E

Q

P

H

650

651

Q

H

A

M

Y

L

R

L

M

T

E

V

A

W

T

K

D

E

L

K

E

A

L

675

676

D

V

T

L

P

R

L

K

A

F

I

P

Q

L

S

R

L

H

I

E

A

L

700

701

H

G

N

I

T

K

Q

A

L

G

I

M

Q

M

V

E

D

T

L

I

E

H

A

H

725

726

T

K

P

L

P

S

Q

L

V

R

Y

R

E

V

Q

L

P

D

R

G

W

F

V

Y

750

751

Q

R

N

E

V

H

N

C

G

I

E

I

Y

Q

T

D

M

Q

S

T

S

E

775

776

N

M

F

L

E

L

F

C

Q

I

S

E

P

C

F

N

T

L

R

T

K

E

Q

L

800

801

G

Y

I

V

F

S

G

P

R

A

N

G

I

Q

G

L

R

F

I

Q

S

E

K

825

826

P

H

Y

L

E

S

R

V

E

A

F

L

I

T

M

E

K

S

I

E

D

M

T

E

850

851

E

A

F

Q

K

H

I

Q

A

L

A

I

R

L

D

K

P

K

L

S

A

E

C

875

876

A

K

Y

W

G

E

I

S

Q

Y

N

F

D

R

D

N

T

E

V

A

Y

L

K

900

901

T

L

T

K

E

D

I

K

F

Y

K

E

M

L

A

V

D

A

P

R

H

K

V

925

926

S

V

H

V

L

A

R

E

M

D

S

C

P

V

G

E

F

P

C

Q

N

D

I

N

950

951

L

S

Q

A

P

A

L

P

Q

P

E

V

I

Q

N

M

T

E

F

K

R

G

L

P

L

975

976

F

P

L

V

K

P

H

I

N

F

M

A

K

L

990

Chain 2

1

M

H

A

G

I

P

M

N

P

A

I

K

R

I

G

N

H

I

25

26

T

K

S

P

E

D

K

R

E

Y

R

G

L

E

L

A

N

G

I

K

V

L

I

S

50

51

D

P

T

D

K

S

A

L

D

V

H

I

G

S

L

S

D

P

N

I

A

75

76

G

L

S

H

F

C

Q

H

M

L

F

L

G

T

K

Y

P

K

E

N

E

Y

S

Q

100

101

F

L

S

E

H

A

G

S

N

A

F

T

S

G

E

H

T

N

Y

F

D

V

S

125

126

H

E

H

L

E

G

A

L

D

R

F

A

Q

F

L

C

P

L

F

D

E

S

C

K

150

151

D

R

E

V

N

A

V

D

S

E

H

E

K

N

V

M

N

D

A

W

R

L

F

Q

L

175

176

E

K

A

T

G

N

P

K

H

P

F

S

K

F

G

T

G

N

K

Y

T

L

E

T

R

200

201

P

N

Q

E

G

I

D

V

R

Q

E

L

K

F

H

S

A

Y

S

N

L

M

225

226

A

V

C

V

L

G

R

E

S

L

D

L

T

N

L

V

K

L

F

S

E

V

E

250

251

N

K

N

V

P

L

P

E

F

P

E

H

P

F

Q

E

H

L

K

Q

L

Y

K

I

275

276

V

P

I

K

D

I

R

N

L

Y

V

T

F

P

I

P

D

L

Q

K

Y

K

S

N

300

301

P

G

H

Y

L

G

H

L

I

G

H

E

G

P

G

S

L

S

E

L

K

S

K

G

325

326

W

V

N

T

L

V

G

Q

K

E

G

A

R

G

F

M

F

I

N

V

D

L

350

351

T

E

G

L

H

V

E

D

I

L

H

M

F

Q

Y

I

Q

K

L

R

A

E

375

376

G

P

Q

E

W

V

F

Q

E

C

K

D

L

N

A

V

A

F

R

F

K

D

K

E

R

400

401

P

R

G

Y

T

S

K

I

A

G

I

L

H

Y

P

L

E

V

L

T

A

E

Y

425

426

L

E

F

R

P

D

L

I

E

M

V

L

D

K

L

R

P

E

N

V

R

V

A

450

451

I

V

S

K

S

F

E

G

K

T

D

R

T

E

W

Y

G

T

Q

Y

K

Q

E

A

475

476

I

P

D

E

V

I

K

W

Q

N

A

D

L

N

G

K

F

K

L

P

T

K

N

E

500

501

F

I

P

T

N

F

E

I

L

P

L

E

K

E

A

T

P

Y

P

A

L

I

K

D

T

525

526

A

M

S

K

L

W

F

K

Q

D

K

F

L

P

K

A

C

L

N

F

E

F

550

551

S

P

F

A

Y

V

D

P

L

H

C

N

M

A

Y

L

Y

L

E

L

K

D

S

L

575

576

N

E

Y

A

Y

A

E

L

A

G

L

S

Y

D

L

Q

N

T

I

Y

G

M

Y

L

600

601

S

V

K

G

Y

N

D

K

Q

P

I

L

K

I

E

K

M

A

T

F

E

I

625

626

D

E

K

R

F

E

I

K

E

A

Y

M

R

S

L

N

F

R

A

E

Q

P

H

650

651

Q

H

A

M

Y

L

R

L

M

T

E

V

A

W

T

K

D

E

L

K

E

A

L

675

676

D

V

T

L

P

R

L

K

A

F

I

P

Q

L

S

R

L

H

I

E

A

L

700

701

H

G

N

I

T

K

Q

A

L

G

I

M

Q

M

V

E

D

T

L

I

E

H

A

H

725

726

T

K

P

L

P

S

Q

L

V

R

Y

R

E

V

Q

L

P

D

R

G

W

F

V

Y

750

751

Q

R

N

E

V

H

N

C

G

I

E

I

Y

Q

T

D

M

Q

S

T

S

E

775

776

N

M

F

L

E

L

F

C

Q

I

S

E

P

C

F

N

T

L

R

T

K

E

Q

L

800

801

G

Y

I

V

F

S

G

P

R

A

N

G

I

Q

G

L

R

F

I

Q

S

E

K

825

826

P

H

Y

L

E

S

R

V

E

A

F

L

I

T

M

E

K

S

I

E

D

M

T

E

850

851

E

A

F

Q

K

H

I

Q

A

L

A

I

R

L

D

K

P

K

L

S

A

E

C

875

876

A

K

Y

W

G

E

I

S

Q

Y

N

F

D

R

D

N

T

E

V

A

Y

L

K

900

901

T

L

T

K

E

D

I

K

F

Y

K

E

M

L

A

V

D

A

P

R

H

K

V

925

926

S

V

H

V

L

A

R

E

M

D

S

C

P

V

G

E

F

P

C

Q

N

D

I

N

950

951

L

S

Q

A

P

A

L

P

Q

P

E

V

I

Q

N

M

T

E

F

K

R

G

L

P

L

975

976

F

P

L

V

K

P

H

I

N

F

M

A

K

L

990

Chain 3

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

F

A

E

D

V

G

25

26

S

N

K

G

A

I

G

L

M

V

G

V

40

Chain 4

1

D

A

E

F

R

H

D

S

G

Y

E

V

H

Q

K

L

V

F

A

E

D

V

G

25

26

S

N

K

G

A

I

G

L

M

V

G

V

40

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40)

Crystal structure of human insulin-degrading enzyme in complex with amyloid-Beta (1-40). Insulin-degrading enzyme (IDE), a Zn2+-metalloprotease, is involved in the clearance of insulin and amyloid-Beta. Loss-of-function mutations of IDE in rodents cause glucose intolerance and cerebral accumulation of amyloid-Beta.

Literature

PMID:	17051221
Author(s):	Shen, Y., Joachimiak, A., Rosner, M.R., Tang, W.J.
Reference:	Nature. 2006 Oct 19;443(7113):870-4. Epub 2006 Oct 11

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	amyloid-beta
Alternative Name:	Abeta-degrading protease, Insulin protease, Insulysin & ABPP, APPI, Alzheimer disease amyloid protein, Amyloid precursor protein, Amyloid-beta precursor protein, Cerebral vascular amyloid peptide, PreA4, Protease nexin-II & ABPP, APPI, Alzheimer disease a
Gene Name:	IDE & APP, A4, AD1 & APP, A4, AD1
Sequence Length:	990 , 40 , 40
Species:
Mutation(s):	No
E.C. Number:	3.4.24.56
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	2G47
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.1
R free:	0.223

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
DIO	A	C4 H8 O2	88.11	1,4-DIETHYLENE DIOXIDE	C1COCCO1	RYHBNJHYFVUHQT-UHFFFAOYSA-N
DIO	B	C4 H8 O2	88.11	1,4-DIETHYLENE DIOXIDE	C1COCCO1	RYHBNJHYFVUHQT-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

H

A

G

I

P

M

N

P

A

I

K

R

I

G

N

H

I

25

26

T

K

S

P

E

D

K

R

E

Y

R

G

L

E

L

A

N

G

I

K

V

L

I

S

50

51

D

P

T

D

K

S

A

L

D

V

H

I

G

S

L

S

D

P

N

I

A

75

76

G

L

S

H

F

C

Q

H

M

L

F

L

G

T

K

Y

P

K

E

N

E

Y

S

Q

100

101

F

L

S

E

H

A

G

S

N

A

F

T

S

G

E

H

T

N

Y

F

D

V

S

125

126

H

E

H

L

E

G

A

L

D

R

F

A

Q

F

L

C

P

L

F

D

E

S

C

K

150

151

D

R

E

V

N

A

V

D

S

E

H

E

K

N

V

M

N

D

A

W

R

L

F

Q

L

175

176

E

K

A

T

G

N

P

K

H

P

F

S

K

F

G

T

G

N

K

Y

T

L

E

T

R

200

201

P

N

Q

E

G

I

D

V

R

Q

E

L

K

F

H

S

A

Y

S

N

L

M

225

226

A

V

C

V

L

G

R

E

S

L

D

L

T

N

L

V

K

L

F

S

E

V

E

250

251

N

K

N

V

P

L

P

E

F

P

E

H

P

F

Q

E

H

L

K

Q

L

Y

K

I

275

276

V

P

I

K

D

I

R

N

L

Y

V

T

F

P

I

P

D

L

Q

K

Y

K

S

N

300

301

P

G

H

Y

L

G

H

L

I

G

H

E

G

P

G

S

L

S

E

L

K

S

K

G

325

326

W

V

N

T

L

V

G

Q

K

E

G

A

R

G

F

M

F

I

N

V

D

L

350

351

T

E

G

L

H

V

E

D

I

L

H

M

F

Q

Y

I

Q

K

L

R

A

E

375

376

G

P

Q

E

W

V

F

Q

E

C

K

D

L

N

A

V

A

F

R

F

K

D

K

E

R

400

401

P

R

G

Y

T

S

K

I

A

G

I

L

H

Y

P

L

E

V

L

T

A

E

Y

425

426

L

E

F

R

P

D

L

I

E

M

V

L

D

K

L

R

P

E

N

V

R

V

A

450

451

I

V

S

K

S

F

E

G

K

T

D

R

T

E

W

Y

G

T

Q

Y

K

Q

E

A

475

476

I

P

D

E

V

I

K

W

Q

N

A

D

L

N

G

K

F

K

L

P

T

K

N

E

500

501

F

I

P

T

N

F

E

I

L

P

L

E

K

E

A

T

P

Y

P

A

L

I

K

D

T

525

526

A

M

S

K

L

W

F

K

Q

D

K

F

L

P

K

A

C

L

N

F

E

F

550

551

S

P

F

A

Y

V

D

P

L

H

C

N

M

A

Y

L

Y

L

E

L

K

D

S

L

575

576

N

E

Y

A

Y

A

E

L

A

G

L

S

Y

D

L

Q

N

T

I

Y

G

M

Y

L

600

601

S

V

K

G

Y

N

D

K

Q

P

I

L

K

I

E

K

M

A

T

F

E

I

625

626

D

E

K

R

F

E

I

K

E

A

Y

M

R

S

L

N

F

R

A

E

Q

P

H

650

651

Q

H

A

M

Y

L

R

L

M

T

E

V

A

W

T

K

D

E

L

K

E

A

L

675

676

D

V

T

L

P

R

L

K

A

F

I

P

Q

L

S

R

L

H

I

E

A

L

700

701

H

G

N

I

T

K

Q

A

L

G

I

M

Q

M

V

E

D

T

L

I

E

H

A

H

725

726

T

K

P

L

P

S

Q

L

V

R

Y

R

E

V

Q

L

P

D

R

G

W

F

V

Y

750

751

Q

R

N

E

V

H

N

C

G

I

E

I

Y

Q

T

D

M

Q

S

T

S

E

775

776

N

M

F

L

E

L

F

C

Q

I

S

E

P

C

F

N

T

L

R

T

K

E

Q

L

800

801

G

Y

I

V

F

S

G

P

R

A

N

G

I

Q

G

L

R

F

I

Q

S

E

K

825

826

P

H

Y

L

E

S

R

V

E

A

F

L

I

T

M

E

K

S

I

E

D

M

T

E

850

851

E

A

F

Q

K

H

I

Q

A

L

A

I

R

L

D

K

P

K

L

S

A

E

C

875

876

A

K

Y

W

G

E

I

S

Q

Y

N

F

D

R

D

N

T

E

V

A

Y

L

K

900

901

T

L

T

K

E

D

I

K

F

Y

K

E

M

L

A

V

D

A

P

R

H

K

V

925

926

S

V

H

V

L

A

R

E

M

D

S

C

P

V

G

E

F

P

C

Q

N

D

I

N

950

951

L

S

Q

A

P

A

L

P

Q

P

E

V

I

Q

N

M

T

E

F

K

R

G

L

P

L

975

976

F

P

L

V

K

P

H

I

N

F

M

A

K

L

990

Chain 2

1

M

H

A

G

I

P

M

N

P

A

I

K

R

I

G

N

H

I

25

26

T

K

S

P

E

D

K

R

E

Y

R

G

L

E

L

A

N

G

I

K

V

L

I

S

50

51

D

P

T

D

K

S

A

L

D

V

H

I

G

S

L

S

D

P

N

I

A

75

76

G

L

S

H

F

C

Q

H

M

L

F

L

G

T

K

Y

P

K

E

N

E

Y

S

Q

100

101

F

L

S

E

H

A

G

S

N

A

F

T

S

G

E

H

T

N

Y

F

D

V

S

125

126

H

E

H

L

E

G

A

L

D

R

F

A

Q

F

L

C

P

L

F

D

E

S

C

K

150

151

D

R

E

V

N

A

V

D

S

E

H

E

K

N

V

M

N

D

A

W

R

L

F

Q

L

175

176

E

K

A

T

G

N

P

K

H

P

F

S

K

F

G

T

G

N

K

Y

T

L

E

T

R

200

201

P

N

Q

E

G

I

D

V

R

Q

E

L

K

F

H

S

A

Y

S

N

L

M

225

226

A

V

C

V

L

G

R

E

S

L

D

L

T

N

L

V

K

L

F

S

E

V

E

250

251

N

K

N

V

P

L

P

E

F

P

E

H

P

F

Q

E

H

L

K

Q

L

Y

K

I

275

276

V

P

I

K

D

I

R

N

L

Y

V

T

F

P

I

P

D

L

Q

K

Y

K

S

N

300

301

P

G

H

Y

L

G

H

L

I

G

H

E

G

P

G

S

L

S

E

L

K

S

K

G

325

326

W

V

N

T

L

V

G

Q

K

E

G

A

R

G

F

M

F

I

N

V

D

L

350

351

T

E

G

L

H

V

E

D

I

L

H

M

F

Q

Y

I

Q

K

L

R

A

E

375

376

G

P

Q

E

W

V

F

Q

E

C

K

D

L

N

A

V

A

F

R

F

K

D

K

E

R

400

401

P

R

G

Y

T

S

K

I

A

G

I

L

H

Y

P

L

E

V

L

T

A

E

Y

425

426

L

E

F

R

P

D

L

I

E

M

V

L

D

K

L

R

P

E

N

V

R

V

A

450

451

I

V

S

K

S

F

E

G

K

T

D

R

T

E

W

Y

G

T

Q

Y

K

Q

E

A

475

476

I

P

D

E

V

I

K

W

Q

N

A

D

L

N

G

K

F

K

L

P

T

K

N

E

500

501

F

I

P

T

N

F

E

I

L

P

L

E

K

E

A

T

P

Y

P

A

L

I

K

D

T

525

526

A

M

S

K

L

W

F

K

Q

D

K

F

L

P

K

A

C

L

N

F

E

F

550

551

S

P

F

A

Y

V

D

P

L

H

C

N

M

A

Y

L

Y

L

E

L

K

D

S

L

575

576

N

E

Y

A

Y

A

E

L

A

G

L

S

Y

D

L

Q

N

T

I

Y

G

M

Y

L

600

601

S

V

K

G

Y

N

D

K

Q

P

I

L

K

I

E

K

M

A

T

F

E

I

625

626

D

E

K

R

F

E

I

K

E

A

Y

M

R

S

L

N

F

R

A

E

Q

P

H

650

651

Q

H

A

M

Y

L

R

L

M

T

E

V

A

W

T

K

D

E

L

K

E

A

L

675

676

D

V

T

L

P

R

L

K

A

F

I

P

Q

L

S

R

L

H

I

E

A

L

700

701

H

G

N

I

T

K

Q

A

L

G

I

M

Q

M

V

E

D

T

L

I

E

H

A

H

725

726

T

K

P

L

P

S

Q

L

V

R

Y

R

E

V

Q

L

P

D

R

G

W

F

V

Y

750

751

Q

R

N

E

V

H

N

C

G

I

E

I

Y

Q

T

D

M

Q

S

T

S

E

775

776

N

M

F

L

E

L

F

C

Q

I

S

E

P

C

F

N

T

L

R

T

K

E

Q

L

800

801

G

Y

I

V

F

S

G

P

R

A

N

G

I

Q

G

L

R

F

I

Q

S

E

K

825

826

P

H

Y

L

E

S

R

V

E

A

F

L

I

T

M

E

K

S

I

E

D

M

T

E

850

851

E

A

F

Q

K

H

I

Q

A

L

A

I

R

L

D

K

P

K

L

S

A

E

C

875

876

A

K

Y

W

G

E

I

S

Q

Y

N

F

D

R

D

N

T

E

V

A

Y

L

K

900

901

T

L

T

K

E

D

I

K

F

Y

K

E

M

L

A

V

D

A

P

R

H

K

V

925

926

S

V

H

V

L

A

R

E

M

D

S

C

P

V

G

E

F

P

C

Q

N

D

I

N

950

951

L

S

Q

A

P

A

L

P

Q

P

E

V

I

Q

N

M

T

E

F

K

R

G

L

P

L

975

976

F

P

L

V

K

P

H

I

N

F

M

A

K

L

990

Chain 3

1

K

C

N

T

A

T

C

A

T

Q

R

L

A

N

F

L

V

H

S

N

F

G

A

25

26

I

L

S

T

N

V

G

S

N

T

Y

37

Chain 4

1

K

C

N

T

A

T

C

A

T

Q

R

L

A

N

F

L

V

H

S

N

F

G

A

25

26

I

L

S

T

N

V

G

S

N

T

Y

37

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40)

Crystal structure of human insulin-degrading enzyme in complex with amylin. Insulin-degrading enzyme (IDE), a Zn2+-metalloprotease, is involved in the clearance of insulin and amyloid-Beta. Loss-of-function mutations of IDE in rodents cause glucose intolerance and cerebral accumulation of amyloid-Beta.

Literature

PMID:	17051221
Author(s):	Shen, Y., Joachimiak, A., Rosner, M.R., Tang, W.J.
Reference:	Nature. 2006 Oct 19;443(7113):870-4. Epub 2006 Oct 11

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	amylin
Alternative Name:	Abeta-degrading protease, Insulin protease, Insulysin & Amylin, Diabetes-associated peptide, Insulinoma amyloid peptide & Amylin, Diabetes-associated peptide, Insulinoma amyloid peptide
Gene Name:	IDE & IAPP & IAPP
Sequence Length:	990 , 37 , 37
Species:
Mutation(s):	No
E.C. Number:	3.4.24.56
UniProt ID:
Keyword(s):

Structure Information

PDB ID:	2G48
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Monomer - A
PDB Classification:	HYDROLASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	2.6
R free:	0.225

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
DIO	A	C4 H8 O2	88.11	1,4-DIETHYLENE DIOXIDE	C1COCCO1	RYHBNJHYFVUHQT-UHFFFAOYSA-N
DIO	B	C4 H8 O2	88.11	1,4-DIETHYLENE DIOXIDE	C1COCCO1	RYHBNJHYFVUHQT-UHFFFAOYSA-N

Structure

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View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4,4'-dihydroxy-3,3',5,5'-tetrachlorobiphenyl

The efficacy of inhibitor is among the highest observed. This is likely attributable to their high binding affinity and their slow dissociation rates and their non- or positively cooperative TTR binding properties, which are unusual.

Literature

PMID:	15610856
Author(s):	Purkey, H.E., Palaninathan, S.K., Kent, K.C., Smith, C., Safe, S.H., Sacchettini, J.C., Kelly, J.W.
Reference:	Chem Biol. 2004 Dec;11(12):1719-28

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2G5U
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.8
R free:	0.22

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
PCQ	A	C12 H6 Cl4 O2	323.99	3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL	c1c(cc(c(c1Cl)O)Cl)c2cc(c(c(c2)Cl)O)Cl	YCYDXOVJXVALHY-UHFFFAOYSA-N
PCQ	B	C12 H6 Cl4 O2	323.99	3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL	c1c(cc(c(c1Cl)O)Cl)c2cc(c(c(c2)Cl)O)Cl	YCYDXOVJXVALHY-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Hydroxylated polychlorinated biphenyls selectively bind transthyretin in blood and inhibit amyloidogenesis: rationalizing rodent PCB toxicity

The efficacy of inhibitor is among the highest observed. This is likely attributable to their high binding affinity and their slow dissociation rates and their non- or positively cooperative TTR binding properties, which are unusual.

Literature

PMID:	15610856
Author(s):	Purkey, H.E., Palaninathan, S.K., Kent, K.C., Smith, C., Safe, S.H., Sacchettini, J.C., Kelly, J.W.
Reference:	Chem Biol. 2004 Dec;11(12):1719-28

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2G9K
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.85
R free:	0.257

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
NE1	A	C12 H5 Cl5 O	342.43	2',3,3',4',5-PENTACHLOROBIPHENYL-4-OL	c1cc(c(c(c1c2cc(c(c(c2)Cl)O)Cl)Cl)Cl)Cl	YICLFMBHTHJFHZ-UHFFFAOYSA-N
NE1	B	C12 H5 Cl5 O	342.43	2',3,3',4',5-PENTACHLOROBIPHENYL-4-OL	c1cc(c(c(c1c2cc(c(c(c2)Cl)O)Cl)Cl)Cl)Cl	YICLFMBHTHJFHZ-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Human Transthyretin (TTR) Complexed with Hydroxylated polychlorinated Biphenyl-4-hydroxy-3,3',5,4'-tetrachlorobiphenyl

The efficacy of inhibitor is among the highest observed. This is likely attributable to their high binding affinity and their slow dissociation rates and their non- or positively cooperative TTR binding properties, which are unusual.

Literature

PMID:	15610856
Author(s):	Purkey, H.E., Palaninathan, S.K., Kent, K.C., Smith, C., Safe, S.H., Sacchettini, J.C., Kelly, J.W.
Reference:	Chem Biol. 2004 Dec;11(12):1719-28

Download

Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2GAB
Amyloid Category:	Non-amyloid
Type:	Inhibitor complex
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	HORMONE/GROWTH FACTOR
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.85
R free:	0.23800000

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
NE2	A	C12 H6 Cl4 O	307.99	3,3',4',5-TETRACHLOROBIPHENYL-4-OL	c1cc(c(cc1c2cc(c(c(c2)Cl)O)Cl)Cl)Cl	RQGVZEFZWFEKQR-UHFFFAOYSA-N
NE2	B	C12 H6 Cl4 O	307.99	3,3',4',5-TETRACHLOROBIPHENYL-4-OL	c1cc(c(cc1c2cc(c(c(c2)Cl)O)Cl)Cl)Cl	RQGVZEFZWFEKQR-UHFFFAOYSA-N

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Chain 2

1

G

P

T

G

T

G

E

S

K

C

P

L

M

V

K

V

L

D

A

V

R

G

S

P

A

25

26

I

N

V

A

V

H

V

F

R

K

A

D

T

W

E

P

F

A

S

G

K

T

S

50

51

E

S

G

E

L

H

G

L

T

E

F

V

E

G

I

Y

K

V

E

I

D

T

75

76

K

S

Y

W

K

A

L

G

I

S

P

F

H

E

H

A

E

V

F

T

A

N

D

S

100

101

G

P

R

Y

T

I

A

L

S

P

Y

S

Y

S

T

A

V

T

N

P

125

126

K

E

127

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystal structure of Cys10 sulfonated transthyretin

TTR is a protein composed of four identical subunits where each monomer has a single chemically modified cysteine residue (Cys10), There is evidence that these chemical modifications of the SH group alter the stability and the amyloidogenic potential of the protein. The sulfonated form was found to enhance the stability of the native conformation of TTR, avoiding misassembly of the protein leading to amyloid. Consequently, the potential treatment of TTR-type amyloidosis by sulfite has been suggested. 3D structure provides structural insight for the stabilizing effect of sulfite. Each subunit has a Beta-sandwich conformation, with two four stranded Beta-pleated sheets (DAGH and CBEF) and a small Alpha-helix between strands. The sulfonated cysteines have two sulfite oxygens involved in intramonomer hydrogen bonds that bridge Cys10, the amino acid immediately before Beta-strand A, to the amino acids immediately after the edge Beta-strand D.

Literature

PMID:	17175208
Author(s):	Gales, L., Saraiva, M.J., Damas, A.M.
Reference:	Biochim Biophys Acta. 2007 Jan;1774(1):59-64. Epub 2006 Nov 6

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Transthyretin
Alternative Name:	ATTR, Prealbumin, TBPA
Gene Name:	TTR, PALB
Sequence Length:	127
Species:	Homo sapiens
Mutation(s):	C10 sulfonated
E.C. Number:
UniProt ID:	P02766
Keyword(s):	Transthyretin

Structure Information

PDB ID:	2H4E
Amyloid Category:	Non-amyloid
Type:	Protein
Global Stoichiometry:	Homo 4-mer - A4
PDB Classification:	TRANSPORT PROTEIN
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.45
R free:	0.198

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CSU	A	C3 H7 N O5 S2	201.22	CYSTEINE-S-SULFONIC ACID	C([C@@H](C(=O)O)N)SS(=O)(=O)O	NOKPBJYHPHHWAN-REOHCLBHSA-N
CSU	B	C3 H7 N O5 S2	201.22	CYSTEINE-S-SULFONIC ACID	C([C@@H](C(=O)O)N)SS(=O)(=O)O	NOKPBJYHPHHWAN-REOHCLBHSA-N
SO4	B	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

Press 'p' to pause
View interactive contact network
Protein Contacts Atlas

Sequence & Sec. Str.

Chain 1

1

M

G

V

T

I

F

V

A

L

Y

D

Y

E

A

R

T

E

D

L

S

F

K

25

26

K

G

E

R

F

Q

I

N

T

E

G

D

W

E

A

R

S

I

A

T

G

K

50

51

N

G

Y

I

P

S

N

Y

V

A

P

A

D

S

64

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: Loop flexibility and amyloid aggregation.

high-resolution crystal structure of the SH3 domain of the c-Yes oncogen. Comparison with other SH3 domains from the Src family revealed significant deviations in the loop regions. In particular, the n-Src loop, highly flexible and partially disordered, is stabilized in an unusual conformation by the establishment of several intramolecular hydrogen bonds. Additionally, it is the first report of amyloid aggregation by an SH3 domain from the Src family.

Literature

PMID:	17418139
Author(s):	Martin-Garcia, J.M., Luque, I., Mateo, P.L., Ruiz-Sanz, J., Camara-Artigas, A.
Reference:	FEBS Lett. 2007 May 1;581(9):1701-6. Epub 2007 Mar 30

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Tyrosine-protein kinase Yes
Alternative Name:	Proto-oncogene c-Yes, p61-Yes
Gene Name:	YES1, YES
Sequence Length:	64
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:	2.7.10.2
UniProt ID:	P07947
Keyword(s):	Proto-oncogene tyrosine-protein kinase Yes

Structure Information

PDB ID:	2HDA
Amyloid Category:	Amyloid
Type:	Protein
Global Stoichiometry:	Monomer - A
PDB Classification:	TRANSFERASE
Method:	X-RAY DIFFRACTION
Resolution (Å):	1.9
R free:	0.27

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
SO4	A	O4 S -2	96.06	SULFATE ION	[O-]S(=O)(=O)[O-]	QAOWNCQODCNURD-UHFFFAOYSA-L

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

K

C

N

T

A

T

C

A

T

Q

R

L

A

N

F

L

V

R

S

N

L

G

P

25

26

V

L

P

T

N

V

G

S

N

T

Y

X

38

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Three-Dimensional NMR Structure of Rat Islet Amyloid Polypeptide in DPC micelles; rat IAPP forms transient alpha-helical structures but does not progress further to form amyloid fibrils

The high-resolution structure of rat IAPP in the membrane-mimicking detergent micelles composed of dodecylphosphocholine was solved. The structure is characterized by a helical region spanning the residues A5 to S23 and a disordered C-terminus. A distortion in the helix is seen at R18 and S19 that may be involved in receptor binding. Rat IAPP is bound on the surface of the micelle. A comparison to the detergent-bound structures of other IAPP variants indicates that the N-terminal region may play a crucial role in the self-association and toxicity of IAPP by controlling access to the putative dimerization interface on the hydrophobic face of the amphipathic helix.

Literature

PMID:	19456151
Author(s):	Nanga, R.P., Brender, J.R., Xu, J., Hartman, K., Subramanian, V., Ramamoorthy, A.
Reference:	J Am Chem Soc. 2009 Jun 17;131(23):8252-61.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Islet amyloid polypeptide
Alternative Name:	Amylin, Diabetes-associated peptide
Gene Name:	Iapp
Sequence Length:	38
Species:	Rattus norvegicus
Mutation(s):	No
E.C. Number:
UniProt ID:	P12969
Keyword(s):	Islet amyloid polypeptide

Structure Information

PDB ID:	2KJ7
Amyloid Category:	Non-amyloid
Type:	Peptide
Global Stoichiometry:	Monomer - A
PDB Classification:	HORMONE
Method:	SOLUTION NMR
Resolution (Å):
R free:

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
NH2	A	H2 N	16.02	AMINO GROUP	[NH2]	QGZKDVFQNNGYKY-UHFFFAOYAF

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

K

C

N

T

A

T

C

A

T

Q

R

L

A

N

F

L

V

H

S

N

F

G

A

25

26

I

L

S

T

N

V

G

S

N

T

Y

X

38

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

Solution NMR structure of human amylin in SDS micelles at pH 7.3

The structure of the naturally occurring peptide in detergent micelles at a neutral pH. The structure has an overall kinked helix motif, with residues 7-17 and 21-28 in a helical conformation, and with a 3(10) helix from Gly 33-Asn 35. In addition, the angle between the N- and C-terminal helices is constrained to 85Â°. The greater helical content of human IAPP in the amidated versus free acid form is likely to play a role in its aggregation and membrane disruptive activity.

Literature

PMID:	21723249
Author(s):	Nanga, R.P., Brender, J.R., Vivekanandan, S., Ramamoorthy, A.
Reference:	Biochim Biophys Acta. 2011 Oct;1808(10):2337-42.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Islet amyloid polypeptide
Alternative Name:	Amylin, Diabetes-associated peptide, Insulinoma amyloid peptide
Gene Name:	IAPP
Sequence Length:	38
Species:	Homo sapiens
Mutation(s):	No
E.C. Number:
UniProt ID:	P10997
Keyword(s):	Islet amyloid polypeptide

Structure Information

PDB ID:	2L86
Amyloid Category:	Amyloid
Type:	Peptide
Global Stoichiometry:	Monomer - A
PDB Classification:	APOPTOSIS
Method:	SOLUTION NMR
Resolution (Å):
R free:

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
NH2	A	H2 N	16.02	AMINO GROUP	[NH2]	QGZKDVFQNNGYKY-UHFFFAOYAF

Structure

Press 'p' to pause
View interactive contact network

Sequence & Sec. Str.

Chain 1

1

M

K

I

D

A

I

V

G

R

N

S

A

K

D

I

R

T

E

R

A

R

V

Q

L

25

26

G

N

V

T

A

L

H

G

I

R

I

S

D

Q

T

N

S

V

E

T

50

51

V

G

K

G

E

S

R

V

L

I

G

N

E

Y

G

K

G

F

W

D

N

H

75

76

H

79

Chain 2

1

M

K

I

D

A

I

V

G

R

N

S

A

K

D

I

R

T

E

R

A

R

V

Q

L

25

26

G

N

V

T

A

L

H

G

I

R

I

S

D

Q

T

N

S

V

E

T

50

51

V

G

K

G

E

S

R

V

L

I

G

N

E

Y

G

K

G

F

W

D

N

H

75

76

H

79

Chain 3

1

M

K

I

D

A

I

V

G

R

N

S

A

K

D

I

R

T

E

R

A

R

V

Q

L

25

26

G

N

V

T

A

L

H

G

I

R

I

S

D

Q

T

N

S

V

E

T

50

51

V

G

K

G

E

S

R

V

L

I

G

N

E

Y

G

K

G

F

W

D

N

H

75

76

H

79

Chain 4

1

M

K

I

D

A

I

V

G

R

N

S

A

K

D

I

R

T

E

R

A

R

V

Q

L

25

26

G

N

V

T

A

L

H

G

I

R

I

S

D

Q

T

N

S

V

E

T

50

51

V

G

K

G

E

S

R

V

L

I

G

N

E

Y

G

K

G

F

W

D

N

H

75

76

H

79

Chain 5

1

M

K

I

D

A

I

V

G

R

N

S

A

K

D

I

R

T

E

R

A

R

V

Q

L

25

26

G

N

V

T

A

L

H

G

I

R

I

S

D

Q

T

N

S

V

E

T

50

51

V

G

K

G

E

S

R

V

L

I

G

N

E

Y

G

K

G

F

W

D

N

H

75

76

H

79

Helix: Magenta; Strand: Yellow; Coil & Turn: White.

Charged residues and Proline are highlighed in blue.

Description

HADDOCK calculated model of Congo red bound to the HET-s amyloid

Congo red, was studied in complex with an amyloid. The binding interface between Congo red and amyloid fibrils formed by the prion domain of the fungal HET?s protein was characterized at atomic resolution. The dye binds highly site?specifically by interacting with residues flanking a groove in the vicinity of a Beta?arc. The three?dimensional (3D) structure of the fibril is strongly conserved upon the binding of Congo red.

Literature

PMID:	21591034
Author(s):	Schutz, A.K., Soragni, A., Hornemann, S., Aguzzi, A., Ernst, M., Bockmann, A., Meier, B.H.
Reference:	Angew Chem Int Ed Engl. 2011 Jun 20;50(26):5956-60.

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Entry:	CSV JSON
Structure:	PDB CIF FASTA
Contact Network:	CSV JSON

Protein Information

Protein Name:	Heterokaryon incompatibility protein s
Alternative Name:	Small s protein, Vegetative incompatibility protein s
Gene Name:	het-s, small s
Sequence Length:	79
Species:	Podospora anserina
Mutation(s):	No
E.C. Number:
UniProt ID:	Q03689
Keyword(s):	Small s protein

Structure Information

PDB ID:	2LBU
Amyloid Category:	Amyloid
Type:	Fibril
Global Stoichiometry:	Homo 5-mer - A5
PDB Classification:	PROTEIN FIBRIL
Method:	SOLID-STATE NMR
Resolution (Å):
R free:

Ligand Information

Ligand ID	Chain ID	Ligand Formula	Ligand MW	Ligand Name	Ligand SMILES	InChI Key
CGO	B	C32 H22 N6 Na2 O6 S2	696.66	sodium 3,3'-(1E,1'E)-biphenyl-4,4'-diylbis(diazene-2,1-diyl)bis(4-aminonaphthalene-1-sulfonate)	c1cc2c(cc(c(c2cc1)N)/N=N/c3ccc(cc3)c4ccc(cc4)/N=N/c5c(c6c(c(c5)S(=O)(=O)[O-][Na+])cccc6)N)S(=O)(=O)[O-][Na+]

/h1-18H,33-34H2,(H,39,40,41)(H,42,43,44)

/q
2*+1/p-2/b37-35+,38-36+

	IQFVPQOLBLOTPF-HKXUKFGYSA-L

Structure database of aggregation related proteins and peptides

Displaying 91 to 120 records out of 565 records fetched.

PMID:	10524280
Author(s):	Pokkuluri, P.R., Solomon, A., Weiss, D.T., Stevens, F.J., Schiffer, M.
Reference:	Amyloid. 1999 Sep;6(3):165-71