{"method": "X-RAY DIFFRACTION", "mutation_s_field": "No", "ec_number": "", "description": "Small-molecule ligands that displace SAP from amyloid fibrils and thereby expose the fibrils to proteolytic clearance mechanisms hold potential as drugs for the prevention and treatment of amyloidosis. 2'-deoxyadenosine-5'-monophosphate (dAMP) was screened as a novel SAP ligand. The crystal structure of the SAP-dAMP complex reveals a decamer in which all interactions between SAP pentamers are mediated by the ligand. The two calcium ions of SAP are bridged by the dAMP phosphate group and five hydrogen bonds are formed between the protein and the ligand, including specific interactions made by the adenine base. The SAP-dAMP decamer is stabilized mainly by base-stacking of adjacent ligand molecules and possibly by electrostatic interactions involving the dAMP phosphate groups.", "ligstr": "CA:A:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;DA:A:C10 H14 N5 O6 P:331.22:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE:c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N:InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1:KHWCHTKSEGGWEX-RRKCRQDMSA-N;CA:B:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;DA:B:C10 H14 N5 O6 P:331.22:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE:c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N:InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1:KHWCHTKSEGGWEX-RRKCRQDMSA-N;CA:C:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;DA:C:C10 H14 N5 O6 P:331.22:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE:c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N:InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1:KHWCHTKSEGGWEX-RRKCRQDMSA-N;CA:D:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;DA:D:C10 H14 N5 O6 P:331.22:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE:c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N:InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1:KHWCHTKSEGGWEX-RRKCRQDMSA-N;CA:E:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;DA:E:C10 H14 N5 O6 P:331.22:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE:c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N:InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1:KHWCHTKSEGGWEX-RRKCRQDMSA-N", "pmid": "9217261", "remarks": "Crystal structure of a decameric complex of human serum amyloid P component with bound dAMP", "amyloid_non_amyloid": "Non-amyloid", "type": "Inhibitor complex", "inchi": "InChI=1S/Ca/q+2%%InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1%%InChI=1S/Ca/q+2%%InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1%%InChI=1S/Ca/q+2%%InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1%%InChI=1S/Ca/q+2%%InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1%%InChI=1S/Ca/q+2%%InChI=1S/C10H14N5O6P/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(21-7)2-20-22(17,18)19/h3-7,16H,1-2H2,(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1", "resolution": "2.8", "species": "Homo sapiens", "secondary_structure": "HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCSCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSEEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSEEGGGBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTTEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGBCEEEESSCEEEECCCC", "chain_id": "A%%A%%B%%B%%C%%C%%D%%D%%E%%E", "gene_names": "APCS, PTX2", "r_value_free": "0.252", "pdb_id": "1LGN", "reference": "J Mol Biol. 1997 Jun 20;269(4):570-8", "keyword": "SERUM AMYLOID P COMPONENT", "protein_name": "Serum amyloid P-component", "ligand_formula": "Ca 2%%C10 H14 N5 O6 P%%Ca 2%%C10 H14 N5 O6 P%%Ca 2%%C10 H14 N5 O6 P%%Ca 2%%C10 H14 N5 O6 P%%Ca 2%%C10 H14 N5 O6 P", "peptide_protein_sequence": "chain-ID A: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID B: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID C: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID D: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID E: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV", "entry": "S-0041", "length": "204", "uniprot_ac": "P02743", "author": "Hohenester, E., Hutchinson, W.L., Pepys, M.B., Wood, S.P.", "ligand_smiles": "[Ca+2]%%c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N%%[Ca+2]%%c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N%%[Ca+2]%%c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N%%[Ca+2]%%c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N%%[Ca+2]%%c1nc(c2c(n1)n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N", "ligand_mw": "40.08%%331.22%%40.08%%331.22%%40.08%%331.22%%40.08%%331.22%%40.08%%331.22", "alternative_name": "9.5S alpha-1-glycoprotein", "ligand_name": "CALCIUM ION%%2'-DEOXYADENOSINE-5'-MONOPHOSPHATE%%CALCIUM ION%%2'-DEOXYADENOSINE-5'-MONOPHOSPHATE%%CALCIUM ION%%2'-DEOXYADENOSINE-5'-MONOPHOSPHATE%%CALCIUM ION%%2'-DEOXYADENOSINE-5'-MONOPHOSPHATE%%CALCIUM ION%%2'-DEOXYADENOSINE-5'-MONOPHOSPHATE", "pdb_classification": "SERUM PROTEIN", "global_stoichiometry": "Homo 5-mer - A5", "inchi_key": "BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%KHWCHTKSEGGWEX-RRKCRQDMSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%KHWCHTKSEGGWEX-RRKCRQDMSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%KHWCHTKSEGGWEX-RRKCRQDMSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%KHWCHTKSEGGWEX-RRKCRQDMSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%KHWCHTKSEGGWEX-RRKCRQDMSA-N", "ligand_id": "CA%%DA%%CA%%DA%%CA%%DA%%CA%%DA%%CA%%DA"}