1N1G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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

  • DOI: 10.1016/s1074-5521(02)00243-0
  • Primary Citation of Related Structures:  
    1N1G, 1JDJ, 1M67, 1M66

  • 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), are considered attractive drug targets ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
glycerol-3-phosphate dehydrogenaseA366Leishmania mexicanaMutation(s): 0 
Gene Names: GPD
EC: 1.1.1.8
Find proteins for P90551 (Leishmania mexicana)
Explore P90551 
Go to UniProtKB:  P90551
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
E [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
BCP
Query on BCP

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]2-BROMO-6-CHLORO-PURINE
C5 H2 Br Cl N4
VLGHYTLGJNPTEN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BCPIC50:  5000000   nM  Binding MOAD
BCPIC50 :  5000000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.421α = 90
b = 70.421β = 90
c = 210.908γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALAdata scaling
AMoREphasing
REFMACrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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