PDB Entry (5zwf) |
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PDB ID: 5zwf | Resolution: 2.1 Å | Exp. Method: X-RAY DIFFRACTION |
PMID: 29936834 | DOI: 10.1021/acs.jmedchem.8b00774 | |
Protein |
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Protein Name: Vitamin D3 receptor | |
Uniprot ID/ACC: P13053 (VDR_RAT) | Organism: Rattus norvegicus (Rat) |
Gene Symbol: Vdr | Gene ID: 24873 |
Protein Class: SIGNALING PROTEIN |
Ligand |
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Ligand Name: 7-[(1R,3R,7E,17beta)-1,3-Dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]-oct-2-en-4-one | ||
Canonical SMILES: C/C=C/C(=O)CC[C@@H](C)[C@H]1CC[C@H]([C@@]12C)/C(CCC2)=C/C=C3\C[C@@H](O)C(=C)[C@H](O)C3 | ||
Standard InChI: InChI=1S/C27H40O3/c1-5-7-22(28)12-9-18(2)23-13-14-24-21(8-6-15-27(23,24)4)11-10-20-16-25(29)19(3)26(30)17-20/h5,7,10-11,18,23-26,29-30H,3,6,8-9,12-17H2,1-2,4H3/b7-5+,21-11+/t18-,23-,24+,25-,26-,27-/m1/s1 | ||
HET Code: 9KR | PubChem: 137348836 | |
DrugBank: - | ChEMBL: CHEMBL4176693 | |
Molecular Formula: C27H40O3 | Mol. Weight: 412.29776 | logP: 5.6889 |
HBD: 2 | HBA: 3 | |
#Rotatable Bonds: 6 | TPSA: 57.53 |
Covalent Mechanism |
Reaction Name | Residue | Chain ID | SASA | pKa | Warhead Name | Warhead Structure |
Michael Addition | HIS 301 | A | 31.46 | 2.43 | Vinyl Carbonyl |
Binding Affinity |
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Database Name | Value |
PDBBind | IC50 : 1.8 nM |