Structure of PDB 5nmb Chain A2 Binding Site BS02

Receptor Information
>5nmb Chain A2 (length=238) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRLSMLPHLADLVSY
SIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSW
SCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAI
CLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLA
DLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV
Ligand information
Ligand ID9CZ
InChIInChI=1S/C28H44O4/c1-17-20(15-21(29)16-24(17)30)9-8-19-7-6-14-28(5)22(10-11-23(19)28)18(2)25-12-13-26(32-25)27(3,4)31/h8-9,18,21-26,29-31H,1,6-7,10-16H2,2-5H3/b19-8+,20-9-/t18-,21+,22+,23-,24-,25-,26+,28+/m0/s1
InChIKeyDDIWZQGTNVZJGO-XOJGNBOJSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C)C4CCC(O4)C(C)(C)O
CACTVS 3.385C[C@H]([C@@H]1CC[C@@H](O1)C(C)(C)O)[C@H]2CC[C@H]3/C(CCC[C@]23C)=C/C=C4/C[C@@H](O)C[C@H](O)C4=C
CACTVS 3.385C[CH]([CH]1CC[CH](O1)C(C)(C)O)[CH]2CC[CH]3C(CCC[C]23C)=CC=C4C[CH](O)C[CH](O)C4=C
OpenEye OEToolkits 2.0.6C[C@@H]([C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C/3\C[C@H](C[C@@H](C3=C)O)O)C)[C@@H]4CC[C@@H](O4)C(C)(C)O
FormulaC28 H44 O4
Name
ChEMBL
DrugBank
ZINC
PDB chain5nmb Chain A2 Residue 4000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5nmb Structure-activity relationship study of vitamin D analogs with oxolane group in their side chain.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		Y175 L258 V262 S265 I299 R302 S303 S306 W314 V328 H333 H423
Binding residue
(residue number reindexed from 1)		Y22 L44 V48 S51 I85 R88 S89 S92 W100 V114 H119 H209
Annotation score1
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
Cellular Component
GO:0005634 nucleus

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nmb, PDBe:5nmb, PDBj:5nmb
PDBsum5nmb
PubMed28399453
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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