{"resolution": "3.0", "ligand_mw": "40.08%%40.08%%40.08%%462.4%%40.08%%40.08%%40.08%%40.08%%40.08%%462.4%%40.08%%462.4%%40.08", "secondary_structure": "HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBCEEEEEEEEECCCSSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSBCSSSBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSSEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEECTTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSBCSSSBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCSSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSEEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSEETTBBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEEECCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTTEEEEEESSCBCCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSBCGGGBEEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBCEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTTEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCTTTCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSEETTSBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CCCCTTEEEEBCSCCSSCEEEECCCCCSCBCSEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTTEEEEEETTEECCCEECCTTCCBCSSCEEEESSCBSSSSCCBCGGGCCCBEEEEEEEESSCCCHHHHHHHHHTCCCCCSSBBTTBCCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCCSSEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEECTTTCEEEEEETTEECCCEECCTTCCCCSSEEEEESSCCSBTTBCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSBBTTBBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTBSSSEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSEEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHTTCCCCCSSEETTBBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CBCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTTEEEEEETTEECCCEECCTTCCBCSSCEEEESSCBSSSSCCBCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGBCEEEESSCEEEECCCC&HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV#CCCCTTEEEEECSCCSSCEEEECCCCCSCBSEEEEEEEEECCCCSCEEEEEEEETTEEEEEEEEEEETTEEEEEETTEEEEEECCCCSSCCEEEEEEEETTTCEEEEEETTEECCCEECCTTCCBCSSCEEEESSCCSSSSCCCCGGGCCCEEEEEEEEESSCCCHHHHHHHHHTCCCCCSSEEGGGCCEEEESSCEEEECCCC", "inchi": "InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+%%InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/Ca/q+2%%InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+%%InChI=1S/Ca/q+2%%InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+%%InChI=1S/Ca/q+2", "method": "X-RAY DIFFRACTION", "ec_number": "", "uniprot_ac": "P02743", "remarks": "Decameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy- 2-methyl-1,3-dioxane]- 5-yloxycarbonyl}-piperazine", "description": "SAP, a protein of the human innate immune system, is universally present in amyloids. Removal of SAP through a specific aggregation mechanism mediated by multivalent ligands appears to provide therapeutic benefit in the progression of this disease. Crystallographic studies reveal that in our novel series of ligands only the methyl and carboxylate moieties of the pyruvate ketal directly interact with the protein, but the geometric constraints imposed by the tether dictate which of two chair conformations are adopted by the pyruvate dioxane ring. Solution studies, as interpreted through a simple thermodynamic model, account for the distribution of pentameric and decameric bound states at different ligand concentrations and indicate that differences in the flexibility of the tether determine the geometry and stability of the specific aggregates formed between SAP and two different bivalent ligands.", "type": "Aggregating complex", "ligand_smiles": "[Ca+2]%%[Ca+2]%%[Ca+2]%%CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O%%[Ca+2]%%[Ca+2]%%[Ca+2]%%[Ca+2]%%[Ca+2]%%CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O%%[Ca+2]%%CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O%%[Ca+2]", "chain_id": "A%%B%%C%%C%%D%%E%%F%%G%%H%%H%%I%%I%%J", "species": "Homo sapiens", "keyword": "Serum amyloid P-component", "ligstr": "CA:A:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:B:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:C:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CPK:C:C18 H26 N2 O12:462.4:BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE:CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O:InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+:GNQQJZKGGHOMBD-RDAHUFKRSA-N;CA:D:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:E:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:F:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:G:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CA:H:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CPK:H:C18 H26 N2 O12:462.4:BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE:CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O:InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+:GNQQJZKGGHOMBD-RDAHUFKRSA-N;CA:I:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N;CPK:I:C18 H26 N2 O12:462.4:BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE:CC1(OCC(CO1)OC(=O)N2CCN(CC2)C(=O)OC3COC(OC3)(C)C(=O)O)C(=O)O:InChI=1S/C18H26N2O12/c1-17(13(21)22)27-7-11(8-28-17)31-15(25)19-3-5-20(6-4-19)16(26)32-12-9-29-18(2,14(23)24)30-10-12/h11-12H,3-10H2,1-2H3,(H,21,22)(H,23,24)/t11-,12-,17+,18+:GNQQJZKGGHOMBD-RDAHUFKRSA-N;CA:J:Ca 2:40.08:CALCIUM ION:[Ca+2]:InChI=1S/Ca/q+2:BHPQYMZQTOCNFJ-UHFFFAOYSA-N", "pmid": "16036920", "mutation_s_field": "No", "author": "Ho, J.G., Kitov, P.I., Paszkiewicz, E., Sadowska, J., Bundle, D.R., Ng, K.K.", "pdb_id": "2A3X", "amyloid_non_amyloid": "Non-amyloid", "inchi_key": "BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%GNQQJZKGGHOMBD-RDAHUFKRSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%GNQQJZKGGHOMBD-RDAHUFKRSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N%%GNQQJZKGGHOMBD-RDAHUFKRSA-N%%BHPQYMZQTOCNFJ-UHFFFAOYSA-N", "ligand_name": "CALCIUM ION%%CALCIUM ION%%CALCIUM ION%%BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE%%CALCIUM ION%%CALCIUM ION%%CALCIUM ION%%CALCIUM ION%%CALCIUM ION%%BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE%%CALCIUM ION%%BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBONYL}-PIPERAZINE%%CALCIUM ION", "ligand_formula": "Ca 2%%Ca 2%%Ca 2%%C18 H26 N2 O12%%Ca 2%%Ca 2%%Ca 2%%Ca 2%%Ca 2%%C18 H26 N2 O12%%Ca 2%%C18 H26 N2 O12%%Ca 2", "ligand_id": "CA%%CA%%CA%%CPK%%CA%%CA%%CA%%CA%%CA%%CPK%%CA%%CPK%%CA", "r_value_free": "0.282", "protein_name": "Serum amyloid P-component", "gene_names": "APCS, PTX2", "global_stoichiometry": "Homo 10-mer - A10", "alternative_name": "9.5S alpha-1-glycoprotein", "peptide_protein_sequence": "chain-ID A: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID B: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID C: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID D: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID E: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID F: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID G: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID H: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID I: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV; chain-ID J: HTDLSGKVFVFPRESVTDHVNLITPLEKPLQNFTLCFRAYSDLSRAYSLFSYNTQGRDNELLVYKERVGEYSLYIGRHKVTSKVIEKFPAPVHICVSWESSSGIAEFWINGTPLVKKGLRQGYFVEAQPKIVLGQEQDSYGGKFDRSQSFVGEIGDLYMWDSVLPPENILSAYQGTPLPANILDWQALNYEIRGYVIIKPLVWV", "pdb_classification": "METAL BINDING PROTEIN", "reference": "J Biol Chem. 2005 Sep 9;280(36):31999-2008. Epub  2005 Jul 20", "length": "204", "entry": "S-0081"}