Structure of PDB 3dzy Chain A Binding Site BS04

Receptor Information
>3dzy Chain A (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHICAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDK
RQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEVESTSSANEDMP
VERILEAELAPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRA
GWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTEL
VSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAY
CKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLME
ML
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 chain3dzy Chain A Residue 463 [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]
PDB3dzy Structure of the intact PPAR-gamma-RXR- nuclear receptor complex on DNA.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		I268 Q275 F313 R316 A327 C432
Binding residue
(residue number reindexed from 1)		I115 Q122 F160 R163 A174 C279
Annotation score1
Binding affinityBindingDB: EC50=100nM,Ki=583nM,IC50=32nM,Kd=240nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific
GO:0001221 transcription coregulator binding
GO:0001972 retinoic acid binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003700 DNA-binding transcription factor activity
GO:0003707 nuclear steroid receptor activity
GO:0004879 nuclear receptor activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0019899 enzyme binding
GO:0042277 peptide binding
GO:0042802 identical protein binding
GO:0042809 nuclear vitamin D receptor binding
GO:0043565 sequence-specific DNA binding
GO:0044323 retinoic acid-responsive element binding
GO:0046872 metal ion binding
GO:0050692 DNA binding domain binding
GO:0050693 LBD domain binding
GO:0070644 vitamin D response element binding
GO:1990837 sequence-specific double-stranded DNA binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0002157 positive regulation of thyroid hormone receptor signaling pathway
GO:0006355 regulation of DNA-templated transcription
GO:0009755 hormone-mediated signaling pathway
GO:0010875 positive regulation of cholesterol efflux
GO:0030154 cell differentiation
GO:0030501 positive regulation of bone mineralization
GO:0032411 positive regulation of transporter activity
GO:0032526 response to retinoic acid
GO:0035357 peroxisome proliferator activated receptor signaling pathway
GO:0042789 mRNA transcription by RNA polymerase II
GO:0043401 steroid hormone receptor signaling pathway
GO:0045893 positive regulation of DNA-templated transcription
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0048384 retinoic acid receptor signaling pathway
GO:0070564 positive regulation of vitamin D receptor signaling pathway
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription regulator complex
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0043235 receptor complex
GO:0090575 RNA polymerase II transcription regulator complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dzy, PDBe:3dzy, PDBj:3dzy
PDBsum3dzy
PubMed19043829
UniProtP19793|RXRA_HUMAN Retinoic acid receptor RXR-alpha (Gene Name=RXRA)

[Back to BioLiP]