Structure of PDB 4rmd Chain A Binding Site BS02

Receptor Information
>4rmd Chain A (length=214) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDMPVERILEAELAVEPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPL
DDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGA
IFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALRE
KVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGD
TPIDTFLMEMLEAP
Ligand information
Ligand ID3SW
InChIInChI=1S/C24H34O2/c1-17(2)11-14-23-21(9-6-10-22(23)20-12-13-20)15-18(3)7-5-8-19(4)16-24(25)26/h5,7-8,15-17,20H,6,9-14H2,1-4H3,(H,25,26)/b8-5+,18-7-,19-16+,21-15+
InChIKeySCCVQQDOUFNKGM-RBEOCVBDSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)CCC1=C(CCC/C1=C\C(C)=C/C=C/C(C)=C/C(O)=O)C2CC2
OpenEye OEToolkits 1.7.6CC(C)CCC1=C(CCCC1=CC(=CC=CC(=CC(=O)O)C)C)C2CC2
OpenEye OEToolkits 1.7.6CC(C)CCC\1=C(CCC/C1=C\C(=C/C=C/C(=C/C(=O)O)/C)\C)C2CC2
ACDLabs 12.01O=C(O)\C=C(\C=C\C=C(/C=C1/C(=C(CCC1)C2CC2)CCC(C)C)C)C
CACTVS 3.385CC(C)CCC1=C(CCCC1=CC(C)=CC=CC(C)=CC(O)=O)C2CC2
FormulaC24 H34 O2
Name(2E,4E,6Z,8E)-8-[3-cyclopropyl-2-(3-methylbutyl)cyclohex-2-en-1-ylidene]-3,7-dimethylocta-2,4,6-trienoic acid
ChEMBLCHEMBL3622723
DrugBank
ZINCZINC000035813958
PDB chain4rmd 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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PDB4rmd Conformationally Defined Rexinoids and Their Efficacy in the Prevention of Mammary Cancers.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I268 A271 A272 Q275 F313 R316 L326 A327 V342 F346 C432 H435 L436
Binding residue
(residue number reindexed from 1)		I24 A27 A28 Q31 F69 R72 L82 A83 V98 F102 C188 H191 L192
Annotation score1
Binding affinityMOAD: Kd=35nM
BindingDB: Kd=35nM,EC50=19nM
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:4rmd, PDBe:4rmd, PDBj:4rmd
PDBsum4rmd
PubMed26331194
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

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