Structure of PDB 4pp5 Chain A Binding Site BS02

Receptor Information
>4pp5 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 ID2W0
InChIInChI=1S/C21H24O2/c1-15(7-4-8-16(2)14-21(22)23)13-18-10-6-11-19-17(3)9-5-12-20(18)19/h4-5,7-9,12-14H,6,10-11H2,1-3H3,(H,22,23)/b8-4+,15-7-,16-14+,18-13+
InChIKeyPUNLLTFBKSEJRJ-MLZXBFFUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(/C=C/C=C(C)\C=C\1CCCc2c(C)cccc\12)=C\C(O)=O
CACTVS 3.385CC(C=CC=C(C)C=C1CCCc2c(C)cccc12)=CC(O)=O
OpenEye OEToolkits 1.7.6Cc1cccc\2c1CCC/C2=C\C(=C/C=C/C(=C/C(=O)O)/C)\C
ACDLabs 12.01O=C(O)\C=C(\C=C\C=C(/C=C2/c1cccc(c1CCC2)C)C)C
OpenEye OEToolkits 1.7.6Cc1cccc2c1CCCC2=CC(=CC=CC(=CC(=O)O)C)C
FormulaC21 H24 O2
Name(2E,4E,6Z,8E)-3,7-dimethyl-8-(5-methyl-3,4-dihydronaphthalen-1(2H)-ylidene)octa-2,4,6-trienoic acid
ChEMBLCHEMBL3289657
DrugBank
ZINCZINC000098208329
PDB chain4pp5 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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PDB4pp5 Methyl substitution of a rexinoid agonist improves potency and reveals site of lipid toxicity.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I268 A271 A272 Q275 F313 R316 L326 A327 V342 C432 L436
Binding residue
(residue number reindexed from 1)		I24 A27 A28 Q31 F69 R72 L82 A83 V98 C188 L192
Annotation score1
Binding affinityMOAD: Kd=18nM
PDBbind-CN: -logKd/Ki=7.74,Kd=18nM
BindingDB: Kd=2240nM,EC50=720nM
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:4pp5, PDBe:4pp5, PDBj:4pp5
PDBsum4pp5
PubMed24801499
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

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