Structure of PDB 3wt5 Chain A Binding Site BS02

Receptor Information
>3wt5 Chain A (length=240) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMSPLSMLPHLADLV
SYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDM
SWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLM
AICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMI
QKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGN
Ligand information
Ligand IDYA1
InChIInChI=1S/C31H52O3/c1-7-8-10-24(16-18-30(4,5)34)21(2)26-14-15-27-25(11-9-17-31(26,27)6)13-12-23-19-28(32)22(3)29(33)20-23/h12-13,21,24,26-29,32-34H,3,7-11,14-20H2,1-2,4-6H3/b25-13+/t21-,24-,26-,27+,28-,29-,31-/m1/s1
InChIKeyRSXHMKSDJHHTDU-PJSVQGINSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCC(CCC(C)(C)O)C(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
ACDLabs 12.01OC3C(=C)\C(O)C/C(=C\C=C1/CCCC2(C)C(C(C)C(CCCC)CCC(O)(C)C)CCC12)C3
CACTVS 3.385CCCC[CH](CCC(C)(C)O)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
OpenEye OEToolkits 1.7.6CCCC[C@H](CCC(C)(C)O)[C@@H](C)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.385CCCC[C@H](CCC(C)(C)O)[C@@H](C)[C@H]1CC[C@H]2C(/CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
FormulaC31 H52 O3
Name(1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL3264166
DrugBank
ZINCZINC000098209632
PDB chain3wt5 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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PDB3wt5 A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 I264 R270 S271 S274 W282 C284 H301 L309 H393 F418
Binding residue
(residue number reindexed from 1)		Y21 V50 S53 I84 R90 S91 S94 W102 C104 H121 L129 H213 F238
Annotation score1
Binding affinityMOAD: ic50=0.29nM
PDBbind-CN: -logKd/Ki=9.54,IC50=0.29nM
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:3wt5, PDBe:3wt5, PDBj:3wt5
PDBsum3wt5
PubMed24742174
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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