Structure of PDB 6jno Chain D Binding Site BS01

Receptor Information
>6jno Chain D (length=203) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVERILEAELANDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVIL
LRAGWNELLIASFSHRSIAVKDGILLGLHVHRNSAHSAGVGAIFDRVLTE
LVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEA
YCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLM
EML
Ligand information
Ligand IDWY5
InChIInChI=1S/C25H26O5/c1-13-8-18-19(25(4,5)7-6-24(18,2)3)11-15(13)16-9-14-10-17(22(27)28)23(29)30-21(14)12-20(16)26/h8-12,26H,6-7H2,1-5H3,(H,27,28)
InChIKeyUYPOSIGCFZMVDD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc2c(cc1c3cc4c(cc3O)OC(=O)C(=C4)C(=O)O)C(CCC2(C)C)(C)C
CACTVS 3.385Cc1cc2c(cc1c3cc4C=C(C(O)=O)C(=O)Oc4cc3O)C(C)(C)CCC2(C)C
FormulaC25 H26 O5
Name7-oxidanyl-2-oxidanylidene-6-(3,5,5,8,8-pentamethyl-6,7-dihydronaphthalen-2-yl)chromene-3-carboxylic acid
ChEMBLCHEMBL4449685
DrugBank
ZINC
PDB chain6jno Chain A Residue 501 [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]
PDB6jno Competitive Binding Assay with an Umbelliferone-Based Fluorescent Rexinoid for Retinoid X Receptor Ligand Screening.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		R302 W305 L433
Binding residue
(residue number reindexed from 1)		R52 W55 L181
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.63,Kd=233nM
BindingDB: Kd=233nM,EC50=22nM,Ki=230nM
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:6jno, PDBe:6jno, PDBj:6jno
PDBsum6jno
PubMed31483660
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

[Back to BioLiP]