4XLD

Crystal structure of the human PPARg-LBD/rosiglitazone complex obtained by dry co-crystallization and in situ diffraction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BRLClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Combining `dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.

Gelin, M.Delfosse, V.Allemand, F.Hoh, F.Sallaz-Damaz, Y.Pirocchi, M.Bourguet, W.Ferrer, J.L.Labesse, G.Guichou, J.F.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1777-1787

  • DOI: https://doi.org/10.1107/S1399004715010342
  • Primary Citation of Related Structures:  
    3RDC, 4XLD, 4XN6, 4XNC, 4XNE, 4XOY, 4XOZ, 4XP0, 4XP2, 4XP3, 4XRJ, 4XRL, 4ZSC, 4ZSD

  • PubMed Abstract: 

    X-ray crystallography is an established technique for ligand screening in fragment-based drug-design projects, but the required manual handling steps - soaking crystals with ligand and the subsequent harvesting - are tedious and limit the throughput of the process. Here, an alternative approach is reported: crystallization plates are pre-coated with potential binders prior to protein crystallization and X-ray diffraction is performed directly 'in situ' (or in-plate). Its performance is demonstrated on distinct and relevant therapeutic targets currently being studied for ligand screening by X-ray crystallography using either a bending-magnet beamline or a rotating-anode generator. The possibility of using DMSO stock solutions of the ligands to be coated opens up a route to screening most chemical libraries.


  • Organizational Affiliation

    CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peroxisome proliferator-activated receptor gamma296Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL

Download Ideal Coordinates CCD File 
C [auth A]2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL)
C18 H19 N3 O3 S
YASAKCUCGLMORW-HNNXBMFYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
B [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BRL BindingDB:  4XLD Ki: min: 8, max: 59 (nM) from 7 assay(s)
Kd: min: 1.2, max: 3300 (nM) from 3 assay(s)
IC50: min: 7.7, max: 6.00e+4 (nM) from 14 assay(s)
EC50: min: 1, max: 1600 (nM) from 47 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.99α = 90
b = 66.99β = 90
c = 157.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BRLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FRISBIFranceANR-10-INSB-05-01

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description