Structure of PDB 1rdt Chain A Binding Site BS02

Receptor Information
>1rdt Chain A (length=211) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EDMPVERILEAELAVEPDPVTNICQAADKQLFTLVEWAKRIPHFSELPLD
DQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAI
FDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREK
VYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDT
PIDTFLMEMLE
Ligand information
Ligand IDL79
InChIInChI=1S/C25H30O3/c1-24(2)12-13-25(3,4)21-14-16(8-10-20(21)24)18-6-5-7-22-19(18)15-17(28-22)9-11-23(26)27/h5-11,14,17,19,22H,12-13,15H2,1-4H3,(H,26,27)/b11-9+/t17-,19?,22?/m1/s1
InChIKeyWFLQBFXZEVUXMT-UEOKTHRPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1(CCC(c2c1ccc(c2)C3=CC=CC4C3CC(O4)C=CC(=O)O)(C)C)C
OpenEye OEToolkits 1.5.0CC1(CCC(c2c1ccc(c2)C3=CC=CC4C3CC(O4)\C=C\C(=O)O)(C)C)C
ACDLabs 10.04O=C(O)\C=C\C3OC4C=CC=C(c1ccc2c(c1)C(C)(C)CCC2(C)C)C4C3
CACTVS 3.341CC1(C)CCC(C)(C)c2cc(ccc12)C3=CC=C[C@@H]4O[C@@H](C[C@H]34)\C=C\C(O)=O
CACTVS 3.341CC1(C)CCC(C)(C)c2cc(ccc12)C3=CC=C[CH]4O[CH](C[CH]34)C=CC(O)=O
FormulaC25 H30 O3
Name(S)-(2E)-3[4-(5,5,8,8-TETRAMETHYL-5,6,7,8-TETRAHYDRO-2-NAPHTHALENYL)TETRAHYDRO-1-BENZOFURAN-2-YL]-2-PROPENOIC ACID
ChEMBL
DrugBank
ZINC
PDB chain1rdt Chain A Residue 463 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rdt Structure-based design of potent retinoid X receptor alpha agonists.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I268 A272 Q275 W305 L309 F313 R316 L326 A327 V342 I345
Binding residue
(residue number reindexed from 1)		I23 A27 Q30 W60 L64 F68 R71 L81 A82 V97 I100
Annotation score1
Binding affinityMOAD: Ki=6nM
PDBbind-CN: -logKd/Ki=6.70,Ki=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:1rdt, PDBe:1rdt, PDBj:1rdt
PDBsum1rdt
PubMed15056000
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

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