Structure of PDB 5b41 Chain A Binding Site BS02

Receptor Information
>5b41 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]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMPLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMS
WDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMA
ICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQ
KLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDYSV
InChIInChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22-,23+,24-,25-,27-/m1/s1
InChIKeyUHMPCVGLSKFXHR-JUTHDLPNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
CACTVS 3.385C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3
OpenEye OEToolkits 2.0.4C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.385C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
ACDLabs 12.01OC(C)(C)CCCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C
FormulaC27 H44 O3
Name(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol;
2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3
ChEMBLCHEMBL1214620
DrugBank
ZINCZINC000004394163
PDB chain5b41 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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PDB5b41 Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics
Resolution1.89 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 R270 S271 S274 W282 C284 V296 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 V49 S52 R89 S90 S93 W101 C103 V115 H120 H212
Annotation score1
Binding affinityBindingDB: Ki=0.030000nM
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:5b41, PDBe:5b41, PDBj:5b41
PDBsum5b41
PubMed27535484
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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