Structure of PDB 1xdk Chain B Binding Site BS02

Receptor Information
>1xdk Chain B (length=245) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSEL
ATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQ
DTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSA
ICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKI
TDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSEGHEPLTPS
Ligand information
Ligand ID9CR
InChIInChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8-,16-14+
InChIKeySHGAZHPCJJPHSC-ZVCIMWCZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CC(=O)O)C)C
CACTVS 3.370CC1=C(/C=C/C(C)=C\C=C\C(C)=C\C(O)=O)C(C)(C)CCC1
ACDLabs 12.01O=C(O)\C=C(\C=C\C=C(/C=C/C1=C(C)CCCC1(C)C)C)C
CACTVS 3.370CC1=C(C=CC(C)=CC=CC(C)=CC(O)=O)C(C)(C)CCC1
OpenEye OEToolkits 1.7.6CC1=C(C(CCC1)(C)C)/C=C/C(=C\C=C\C(=C\C(=O)O)\C)/C
FormulaC20 H28 O2
Name(9cis)-retinoic acid
ChEMBLCHEMBL705
DrugBankDB00523
ZINCZINC000012661824
PDB chain1xdk Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1xdk CHARACTERIZATION OF THE INTERACTION BETWEEN RAR/RXR HETERODIMERS AND TRANSCRIPTIONAL COACTIVATORS THROUGH STRUCTURAL AND FLUORESCENCE ANISOTROPY STUDIES
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A225 C228 L262 I263 I266 F279 S280 G294 F295
Binding residue
(residue number reindexed from 1)		A51 C54 L88 I89 I92 F105 S106 G120 F121
Annotation score1
Binding affinityBindingDB: Kd=7nM
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
GO:0048384 retinoic acid receptor signaling pathway
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:1xdk, PDBe:1xdk, PDBj:1xdk
PDBsum1xdk
PubMed15528208
UniProtP22605|RARB_MOUSE Retinoic acid receptor beta (Gene Name=Rarb)

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