Structure of PDB 6t2m Chain A Binding Site BS02

Receptor Information
>6t2m 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 IDM9Q
InChIInChI=1S/C32H46O5/c1-5-37-30(36)14-16-32(17-18-32)29(35)13-8-21(2)26-11-12-27-23(7-6-15-31(26,27)4)9-10-24-19-25(33)20-28(34)22(24)3/h8-10,13-14,16,21,25-29,33-35H,3,5-7,11-12,15,17-20H2,1-2,4H3/b13-8+,16-14-,23-9+,24-10-/t21-,25-,26-,27+,28+,29-,31-/m1/s1
InChIKeyFUDAEUIGIJZUAY-MRFCKDSNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CCOC(=O)C=CC1(CC1)C(C=CC(C)C2CCC3C2(CCCC3=CC=C4CC(CC(C4=C)O)O)C)O
OpenEye OEToolkits 2.0.7CCOC(=O)/C=C\C1(CC1)[C@@H](/C=C/[C@@H](C)[C@H]2CC[C@@H]\3[C@@]2(CCC/C3=C\C=C/4\C[C@H](C[C@@H](C4=C)O)O)C)O
CACTVS 3.385CCOC(=O)C=CC1(CC1)[CH](O)C=C[CH](C)[CH]2CC[CH]3C(CCC[C]23C)=CC=C4C[CH](O)C[CH](O)C4=C
CACTVS 3.385CCOC(=O)\C=C/C1(CC1)[C@H](O)\C=C\[C@@H](C)[C@H]2CC[C@H]3/C(CCC[C@]23C)=C/C=C\4C[C@@H](O)C[C@H](O)C\4=C
FormulaC32 H46 O5
Nameethyl (~{Z})-3-[1-[(~{E},1~{R},4~{R})-4-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[(2~{Z})-2-[(3~{S},5~{R})-2-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]-1-oxidanyl-pent-2-enyl]cyclopropyl]prop-2-enoate
ChEMBL
DrugBank
ZINC
PDB chain6t2m Chain A 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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PDB6t2m Structural Analysis of VDR Complex with ZK168281 Antagonist.
Resolution3.0 Å
Binding residue
(original residue number in PDB)
Y175 V262 S265 I299 R302 S303 S306 W314 V328 H333 H423 Q426 Y427 L430
Binding residue
(residue number reindexed from 1)
Y22 V49 S52 I86 R89 S90 S93 W101 V115 H120 H210 Q213 Y214 L217
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:6t2m, PDBe:6t2m, PDBj:6t2m
PDBsum6t2m
PubMed32787090
UniProtQ9PTN2|VDRA_DANRE Vitamin D3 receptor A (Gene Name=vdra)

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