Structure of PDB 5xpm Chain A Binding Site BS02

Receptor Information
>5xpm Chain A (length=239) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRSPLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMS
WDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMA
ICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQ
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand ID8C0
InChIInChI=1S/C36H54O4/c1-6-7-9-27(15-20-35(40-5)29-13-16-30(37)17-14-29)24(2)31-18-19-32-28(10-8-21-36(31,32)4)12-11-26-22-33(38)25(3)34(39)23-26/h11-14,16-17,24,27,31-35,37-39H,3,6-10,15,18-23H2,1-2,4-5H3/b28-12+/t24-,27+,31-,32+,33-,34-,35+,36-/m1/s1
InChIKeyAJZMBYIVQYCFHK-WPVJRCGCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCC(CCC(c1ccc(cc1)O)OC)C(C)C2CCC3C2(CCCC3=CC=C4CC(C(=C)C(C4)O)O)C
CACTVS 3.385CCCC[CH](CC[CH](OC)c1ccc(O)cc1)[CH](C)[CH]2CC[CH]3C(CCC[C]23C)=CC=C4C[CH](O)C(=C)[CH](O)C4
OpenEye OEToolkits 2.0.6CCCC[C@@H](CC[C@@H](c1ccc(cc1)O)OC)[C@@H](C)[C@H]2CC[C@@H]\3[C@@]2(CCC/C3=C\C=C4C[C@H](C(=C)[C@@H](C4)O)O)C
CACTVS 3.385CCCC[C@@H](CC[C@H](OC)c1ccc(O)cc1)[C@@H](C)[C@H]2CC[C@H]3C(/CCC[C@]23C)=C/C=C/4C[C@@H](O)C(=C)[C@H](O)C/4
FormulaC36 H54 O4
Name(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol;
22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3
ChEMBL
DrugBank
ZINC
PDB chain5xpm Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xpm Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
Resolution2.2 Å
Binding residue
(original residue number in PDB)
Y143 V230 S233 R270 S271 S274 W282 C284 A299 H301 L305 H393 L400
Binding residue
(residue number reindexed from 1)
Y21 V49 S52 R89 S90 S93 W101 C103 A118 H120 L124 H212 L219
Annotation score1
Binding affinityMOAD: ic50=23nM
PDBbind-CN: -logKd/Ki=7.64,IC50=23nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0004879 nuclear receptor activity
Biological Process
GO:0006355 regulation of DNA-templated transcription

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Molecular Function

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Biological Process
External links
PDB RCSB:5xpm, PDBe:5xpm, PDBj:5xpm
PDBsum5xpm
PubMed28954197
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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