Structure of PDB 8ck5 Chain A Binding Site BS02

Receptor Information
>8ck5 Chain A (length=239) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMLSDEQMQIINSLVEAHHKTYDDSYSDFVRFRPPVRRLSMLPHLADLVS
YSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMS
WSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMA
ICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKL
ADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVFGSEV
Ligand information
Ligand IDUYO
InChIInChI=1S/C27H43NO4/c1-18(8-6-14-26(3,4)28(31)32)23-12-13-24-20(9-7-15-27(23,24)5)10-11-21-16-22(29)17-25(30)19(21)2/h10-11,18,22-25,29-30H,2,6-9,12-17H2,1,3-5H3/b20-10+,21-11-/t18-,22-,23-,24+,25+,27-/m1/s1
InChIKeySSROHWHVGDBOBJ-NKMMMXOESA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](CCCC(C)(C)[N](=O)=O)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C\3C[C@@H](O)C[C@H](O)C\3=C
CACTVS 3.385C[CH](CCCC(C)(C)[N](=O)=O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C[CH](O)C3=C
OpenEye OEToolkits 2.0.7CC(CCCC(C)(C)N(=O)=O)C1CCC2C1(CCCC2=CC=C3CC(CC(C3=C)O)O)C
OpenEye OEToolkits 2.0.7C[C@H](CCCC(C)(C)N(=O)=O)[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
FormulaC27 H43 N O4
Name(1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-nitro-heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol;
25-nitro derivative of 1,25D3
ChEMBL
DrugBank
ZINC
PDB chain8ck5 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ck5 Structural analysis and biological activities of C25-amino and C25-nitro vitamin D analogs.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		Y175 L258 A259 V262 S265 R302 S303 S306 W314 V328 H333
Binding residue
(residue number reindexed from 1)		Y22 L45 A46 V49 S52 R89 S90 S93 W101 V115 H120
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:8ck5, PDBe:8ck5, PDBj:8ck5
PDBsum8ck5
PubMed37054528
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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