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 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1107/S1399004715010342
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxisome proliferator-activated receptor gamma
A
296Homo sapiensMutation(s): 0 
Gene Names: PPARGNR1C3
Find proteins for P37231 (Homo sapiens)
Go to UniProtKB:  P37231
NIH Common Fund Data Resources
PHAROS  P37231
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRL
Query on BRL

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

Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BRLEC50:  39   nM  BindingDB
BRLEC50:  40   nM  BindingDB
BRLIC50:  1   nM  BindingDB
BRLEC50:  52   nM  BindingDB
BRLKi:  27   nM  BindingDB
BRLIC50:  292   nM  BindingDB
BRLEC50:  87   nM  BindingDB
BRLEC50:  89   nM  BindingDB
BRLEC50:  1100   nM  BindingDB
BRLKi:  47   nM  BindingDB
BRLEC50:  114   nM  BindingDB
BRLEC50:  117   nM  BindingDB
BRLIC50:  38   nM  BindingDB
BRLKd:  0.14000000059604645   nM  BindingDB
BRLEC50:  95   nM  BindingDB
BRLEC50:  10   nM  BindingDB
BRLEC50:  30   nM  BindingDB
BRLIC50:  76   nM  BindingDB
BRLKi:  8   nM  BindingDB
BRLEC50:  316   nM  BindingDB
BRLEC50:  326   nM  BindingDB
BRLEC50:  332   nM  BindingDB
BRLEC50:  300   nM  BindingDB
BRLEC50:  1   nM  BindingDB
BRLEC50:  260   nM  BindingDB
BRLKd:  1.2000000476837158   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • 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



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Database references