PDB Entry (5zwh)
PDB ID: 5zwh Resolution: 2.38 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:   2-[(1R,3R,7E,17beta)-1,3-Dihydroxy-2-methylidene-9,10-secoestra-5,7-dien-17-yl]-oct-6-en-4-yn-3-one
Canonical SMILES:   C/C=C/C#CC(=O)[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/C27H36O3/c1-5-6-7-10-24(28)18(2)22-13-14-23-21(9-8-15-27(22,23)4)12-11-20-16-25(29)19(3)26(30)17-20/h5-6,11-12,18,22-23,25-26,29-30H,3,8-9,13-17H2,1-2,4H3/b6-5+,21-12+/t18-,22+,23-,25+,26+,27+/m0/s1
HET Code:   9KX PubChem:   134693766
DrugBank:   - ChEMBL:   -
Molecular Formula:   C27H36O3 Mol. Weight:   408.26645 logP:   4.9121
HBD:   2 HBA:   3
#Rotatable Bonds:   3 TPSA:   57.53
Covalent Mechanism
Reaction Name Residue Chain ID SASA pKa Warhead Name Warhead Structure
Michael Addition HIS 301 A 41.74 1.25 Propargyl Carbonyl
Binding Affinity
-