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 

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Ligand Structure Quality Assessment 


This is version 1.3 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

  • DOI: https://doi.org/10.1016/s0014-5793(02)02700-x
  • Primary Citation of Related Structures:  
    1K3T

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase
A, B, C, D
359Trypanosoma cruziMutation(s): 0 
EC: 1.2.1.12
UniProt
Find proteins for P22513 (Trypanosoma cruzi)
Explore P22513 
Go to UniProtKB:  P22513
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22513
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BRZ
Query on BRZ

Download Ideal Coordinates CCD File 
E [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
BRZ PDBBind:  1K3T IC50: 6.40e+4 (nM) from 1 assay(s)
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 = 82.08α = 90
b = 84.97β = 96.32
c = 105.24γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description