Structure of PDB 1xdk Chain A Binding Site BS02

Receptor Information
>1xdk Chain A (length=217) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANEDMPVEKILEAELAVEPPNDPVTNICQAADKQLFTLVEWAKRIPHFSE
LPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAG
VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEA
LREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKL
IGDTPIDTFLMEMLEAP
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 A Residue 500 [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)		A276 Q280 W310 F318 R321 L331 A332 V347 C437 L441
Binding residue
(residue number reindexed from 1)		A30 Q34 W64 F72 R75 L85 A86 V101 C191 L195
Annotation score1
Binding affinityBindingDB: IC50=82nM,Kd=32nM,EC50=200nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003707 nuclear steroid receptor activity
GO:0008270 zinc ion binding
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:1xdk, PDBe:1xdk, PDBj:1xdk
PDBsum1xdk
PubMed15528208
UniProtP28700|RXRA_MOUSE Retinoic acid receptor RXR-alpha (Gene Name=Rxra)

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