1K3T

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi Complexed with Chalepin, a Coumarin Derivative Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Trypanosoma cruzi glycosomal glyceraldehyde-3-phosphate dehydrogenase complexed with chalepin, a natural product inhibitor, at 1.95 A resolution.

Pavao, F.Castilho, M.S.Pupo, M.T.Dias, R.L.Correa, A.G.Fernandes, J.B.da Silva, M.F.Mafezoli, J.Vieira, P.C.Oliva, G.

(2002) FEBS Lett. 520: 13-17


  • PubMed Abstract: 
  • The structure of the glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) from Trypanosoma cruzi complexed with chalepin, a natural product from Pilocarpus spicatus, has been determined by X-ray crystallography to 1.95 A resolution. The struc ...

    The structure of the glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) from Trypanosoma cruzi complexed with chalepin, a natural product from Pilocarpus spicatus, has been determined by X-ray crystallography to 1.95 A resolution. The structure is in the apo form without cofactors in the subunits of the tetrameric gGAPDH in the asymmetric unit. Unequivocal density corresponding to the inhibitor was clearly identified in one monomer. The final refined model of the complex shows extensive conformational changes when compared with the native structure. The mode of binding of chalepin to gGAPDH and its implications for inhibitor design are discussed.


    Related Citations: 
    • Strategies for the Isolation and Identification of Trypanocidal Compounds from the Rutales
      Vieira, P.C.,Mafezoli, J.,Pupo, M.T.,Fernandes, J.B.,Silva, M.F.G.F.,Albuquerque, S.,Oliva, G.,Pavao, F.
      (2001) Pure Appl.Chem. 73: 617
    • Estudos Cristalograficos e Planejamento Racional de Inibidores Especificos da Enzima Gliceraldeido-3-fosfato Desidrogenase Glicossomal (gGAPDH) de Trypanosoma cruzi
      Pavao, F.
      (2001) Thesis --: 1


    Organizational Affiliation

    Instituto de Química de São Carlos, USP, São Carlos, SP, Brazil.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D
359Trypanosoma cruziEC: 1.2.1.12
Find proteins for P22513 (Trypanosoma cruzi)
Go to UniProtKB:  P22513
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRZ
Query on BRZ

Download SDF File 
Download CCD File 
C
6-(1,1-DIMETHYLALLYL)-2-(1-HYDROXY-1-METHYLETHYL)-2,3-DIHYDRO-7H-FURO[3,2-G]CHROMEN-7-ONE
C19 H22 O4
JCDLLLXYAICSQV-INIZCTEOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BRZIC50: 64000 nM BINDINGMOAD
BRZIC50: 64000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.080α = 90.00
b = 84.970β = 96.32
c = 105.240γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-10-04 
  • Released Date: 2002-06-19 
  • Deposition Author(s): Pavao, F.

Revision History 

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance