Structure of PDB 6jez Chain A Binding Site BS02

Receptor Information
>6jez 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 IDYSV
InChIInChI=1S/C27H44O3/c1-18(8-6-14-26(3,4)30)22-12-13-23-21(9-7-15-27(22,23)5)11-10-20-16-24(28)19(2)25(29)17-20/h10-11,18,22-25,28-30H,2,6-9,12-17H2,1,3-5H3/b21-11+/t18-,22-,23+,24-,25-,27-/m1/s1
InChIKeyUHMPCVGLSKFXHR-JUTHDLPNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CC(CCCC(C)(C)O)C1CCC2C1(CCCC2=CC=C3CC(C(=C)C(C3)O)O)C
CACTVS 3.385C[C@H](CCCC(C)(C)O)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C/3C[C@@H](O)C(=C)[C@H](O)C/3
OpenEye OEToolkits 2.0.4C[C@H](CCCC(C)(C)O)[C@H]1CC[C@@H]\2[C@@]1(CCC/C2=C\C=C3C[C@H](C(=C)[C@@H](C3)O)O)C
CACTVS 3.385C[CH](CCCC(C)(C)O)[CH]1CC[CH]2C(CCC[C]12C)=CC=C3C[CH](O)C(=C)[CH](O)C3
ACDLabs 12.01OC(C)(C)CCCC(C)C1CCC2C1(CCCC2=[C@H][C@H]=C3CC(C(\C(C3)O)=C)O)C
FormulaC27 H44 O3
Name(1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol;
2-methylidene-19-nor-1alpha,25-dihydroxyvitamin D3
ChEMBLCHEMBL1214620
DrugBank
ZINCZINC000004394163
PDB chain6jez Chain A Residue 501 [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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PDB6jez Cyclization Reaction-Based Turn-on Probe for Covalent Labeling of Target Proteins.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y143 V230 S233 R270 S271 S274 W282 C284 V296 H301 H393
Binding residue
(residue number reindexed from 1)		Y21 V50 S53 R90 S91 S94 W102 C104 V116 H121 H213
Annotation score1
Binding affinityBindingDB: Ki=0.030000nM
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:6jez, PDBe:6jez, PDBj:6jez
PDBsum6jez
PubMed31991094
UniProtP13053|VDR_RAT Vitamin D3 receptor (Gene Name=Vdr)

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