1N1G

Crystal structure of Leishmania mexicana Glycerol-3-phosphate dehydrogenase with inhibitor BCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Anomalous differences of light elements in determining precise binding modes of ligands to glycerol-3-phosphate dehydrogenase.

Choe, J.Suresh, S.Wisedchaisri, G.Kennedy, K.J.Gelb, M.H.Hol, W.G.

(2002) Chem.Biol. 9: 1189-1197

  • Primary Citation of Related Structures:  1JDJ, 1M66, 1M67

  • PubMed Abstract: 
  • Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), ...

    Pathogenic protozoa such as Trypanosome and Leishmania species cause tremendous suffering worldwide. Because of their dependence on glycolysis for energy, the glycolytic enzymes of these organisms, including glycerol-3-phosphate dehydrogenase (GPDH), are considered attractive drug targets. Using the adenine part of NAD as a lead compound, several 2,6-disubstituted purines were synthesized as inhibitors of Leishmania mexicana GPDH (LmGPDH). The electron densities for the inhibitor 2-bromo-6-chloro-purine bound to LmGPDH using a "conventional" wavelength around 1 A displayed a quasisymmetric shape. The anomalous signals from data collected at 1.77 A clearly indicated the positions of the halogen atoms and revealed the multiple binding modes of this inhibitor. Intriguing differences in the observed binding modes of the inhibitor between very similarly prepared crystals illustrate the possibility of crystal-to-crystal variations in protein-ligand complex structures.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glycerol-3-phosphate dehydrogenase
A
366Leishmania mexicanaGene Names: GPD
EC: 1.1.1.8
Find proteins for P90551 (Leishmania mexicana)
Go to UniProtKB:  P90551
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCP
Query on BCP

Download SDF File 
Download CCD File 
A
2-BROMO-6-CHLORO-PURINE
C5 H2 Br Cl N4
VLGHYTLGJNPTEN-UHFFFAOYSA-N
 Ligand Interaction
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCPIC50: 5000000 nM BINDINGMOAD
BCPIC50: ~5000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.421α = 90.00
b = 70.421β = 90.00
c = 210.908γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
AMoREphasing
HKL-2000data collection
SCALAdata scaling
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2002-10-17 
  • Released Date: 2003-10-28 
  • Deposition Author(s): Choe, J., Hol, W.G.

Revision History 

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance