9CK0

Cocrystal of PPARg LBD and NFKBIB / IKBB peptide with agonist GW1929

  • Classification: DNA BINDING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-07-08 Released: 2024-07-17 
  • Deposition Author(s): Nemetchek, M.D., McClelland, L.J., Hughes, T.S.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.255 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Cocrystal of PPARg LBD with NFKBIB / IKBB peptide containing N-anchor motif LxxLL and agonist GW1929

Nemetchek, M.D., Hughes, T.S.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma276Homo sapiensMutation(s): 0 
Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens)
Explore P37231 
Go to UniProtKB:  P37231
PHAROS:  P37231
GTEx:  ENSG00000132170 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37231
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappa-B inhibitor beta23Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15653 (Homo sapiens)
Explore Q15653 
Go to UniProtKB:  Q15653
PHAROS:  Q15653
GTEx:  ENSG00000104825 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15653
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDK (Subject of Investigation/LOI)
Query on EDK
Download Ideal Coordinates CCD File 
C [auth A](2~{S})-3-[4-[2-[methyl(pyridin-2-yl)amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl)phenyl]amino]propanoic acid
C30 H29 N3 O4
QTQMRBZOBKYXCG-MHZLTWQESA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
EDK BindingDB:  9CK0 Ki: min: 0.05, max: 104 (nM) from 6 assay(s)
EC50: min: 1.5, max: 389 (nM) from 16 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.255 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.53α = 90
b = 89.5β = 90
c = 121.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK129646
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM140963

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release