Structure of PDB 1fby Chain B Binding Site BS01

Receptor Information
>1fby Chain B (length=212) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DMPVERILEAELAVEPDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDD
QVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIF
DRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKV
YASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTP
IDTFLMEMLEAP
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 chain1fby Chain B Residue 1500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1fby Crystal structure of the human RXRalpha ligand-binding domain bound to its natural ligand: 9-cis retinoic acid.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		I1268 A1271 A1272 Q1275 F1313 R1316 L1326 A1327 V1342 C1432
Binding residue
(residue number reindexed from 1)		I22 A25 A26 Q29 F67 R70 L80 A81 V96 C186
Annotation score1
Binding affinityMOAD: Kd=1.5nM
BindingDB: EC50=100nM,Ki=583nM,IC50=32nM,Kd=240nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1fby, PDBe:1fby, PDBj:1fby
PDBsum1fby
PubMed10835357
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

[Back to BioLiP]