4ZSD

Human Cyclophilin D Complexed with an Inhibitor at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.134 

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.,Sect.D 71: 1777-1787

  • DOI: 10.1107/S1399004715010342
  • Primary Citation of Related Structures:  

  • 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.,Université Grenoble Alpes, IBS, 38044 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase F, mitochondrial
A
164Homo sapiensMutation(s): 1 
Gene Names: PPIF (CYP3)
EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens)
Go to Gene View: PPIF
Go to UniProtKB:  P30405
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7I6
Query on 7I6

Download SDF File 
Download CCD File 
A
1-(4-aminobenzyl)-3-[(2S)-4-(methylsulfanyl)-1-{(2R)-2-[2-(methylsulfanyl)phenyl]pyrrolidin-1-yl}-1-oxobutan-2-yl]urea
C24 H32 N4 O2 S2
SXQHCTVKKRKZEF-LEWJYISDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.134 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.943α = 90.00
b = 57.943β = 90.00
c = 88.570γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
Cootmodel building
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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