PDB Entry (5zwf)
PDB ID: 5zwf Resolution: 2.1 Å Exp. Method: X-RAY DIFFRACTION
PMID: 29936834 DOI: 10.1021/acs.jmedchem.8b00774
Protein
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
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
Database Name Value
PDBBind IC50 : 1.8 nM