Structure of PDB 3wt7 Chain A Binding Site BS02

Receptor Information
>3wt7 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 IDYA2
InChIInChI=1S/C32H54O3/c1-7-10-12-26(21-32(35,8-2)9-3)22(4)27-16-17-28-25(13-11-18-31(27,28)6)15-14-24-19-29(33)23(5)30(34)20-24/h14-15,22,26-30,33-35H,5,7-13,16-21H2,1-4,6H3/b25-15+/t22-,26-,27-,28+,29-,30-,31-/m1/s1
InChIKeyOILLQCLQUXHGBN-ZVBNMKQKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCC(CC(CC)(CC)O)C(C)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
OpenEye OEToolkits 1.7.6CCCC[C@H](CC(CC)(CC)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](CC(O)(CC)CC)[C@@H](C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C3C[C@@H](O)C(=C)[C@H](O)C3
ACDLabs 12.01OC3C(=C)\C(O)C/C(=C\C=C1/CCCC2(C)C(C(C)C(CCCC)CC(O)(CC)CC)CCC12)C3
CACTVS 3.385CCCC[CH](CC(O)(CC)CC)[CH](C)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
FormulaC32 H54 O3
Name(1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
ChEMBLCHEMBL3264168
DrugBank
ZINCZINC000098209633
PDB chain3wt7 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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PDB3wt7 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.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y143 L229 S233 R270 S271 S274 W282 C284 V296 H301 H393 Y397
Binding residue
(residue number reindexed from 1)		Y21 L49 S53 R90 S91 S94 W102 C104 V116 H121 H213 Y217
Annotation score1
Binding affinityMOAD: ic50=1.79nM
PDBbind-CN: -logKd/Ki=8.75,IC50=1.79nM
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:3wt7, PDBe:3wt7, PDBj:3wt7
PDBsum3wt7
PubMed24742174
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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