1GYQ

CRYSTAL STRUCTURE OF GLYCOSOMAL GLYCERALDEHYDE FROM LEISHMANIA MEXICANA IN COMPLEX WITH N6-BENZYL-NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-based design of submicromolar, biologically active inhibitors of trypanosomatid glyceraldehyde-3-phosphate dehydrogenase.

Aronov, A.M.Suresh, S.Buckner, F.S.Van Voorhis, W.C.Verlinde, C.L.Opperdoes, F.R.Hol, W.G.Gelb, M.H.

(1999) Proc Natl Acad Sci U S A 96: 4273-4278

  • DOI: 10.1073/pnas.96.8.4273
  • Primary Citation of Related Structures:  
    1GYQ

  • PubMed Abstract: 
  • The bloodstream stage of Trypanosoma brucei and probably the intracellular (amastigote) stage of Trypanosoma cruzi derive all of their energy from glycolysis. Inhibiting glycolytic enzymes may be a novel approach for the development of antitrypanosomatid drugs provided that sufficient parasite versus host selectivity can be obtained ...

    The bloodstream stage of Trypanosoma brucei and probably the intracellular (amastigote) stage of Trypanosoma cruzi derive all of their energy from glycolysis. Inhibiting glycolytic enzymes may be a novel approach for the development of antitrypanosomatid drugs provided that sufficient parasite versus host selectivity can be obtained. Guided by the crystal structures of human, T. brucei, and Leishmania mexicana glyceraldehyde-3-phosphate dehydrogenase, we designed adenosine analogs as tight binding inhibitors that occupy the pocket on the enzyme that accommodates the adenosyl moiety of the NAD+ cosubstrate. Although adenosine is a very poor inhibitor, IC50 approximately 50 mM, addition of substituents to the 2' position of ribose and the N6-position of adenosine led to disubstituted nucleosides with micromolar to submicromolar potency in glyceraldehyde-3-phosphate dehydrogenase assays, an improvement of 5 orders of magnitude over the lead. The designed compounds do not inhibit the human glycolytic enzyme when tested up to their solubility limit (approximately 40 microM). When tested against cultured bloodstream T. brucei and intracellular T. cruzi, N6-(1-naphthalenemethyl)-2'-(3-chlorobenzamido)adenosine inhibited growth in the low micromolar range. Within minutes after adding this compound to bloodstream T. brucei, production of glucose-derived pyruvate ceased, parasite motility was lost, and a mixture of grossly deformed and lysed parasites was observed. These studies underscore the feasibility of using structure-based drug design to transform a mediocre lead compound into a potent enzyme inhibitor. They also suggest that energy production can be blocked in trypanosomatids with a tight binding competitive inhibitor of an enzyme in the glycolytic pathway.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE)A, B, C, D358Leishmania mexicanaMutation(s): 0 
Gene Names: GLYCERALDEHYDE-3-PHOSPHATEURCE 6 DEHYDROGENASEGAPG
EC: 1.2.1.12
UniProt
Find proteins for Q27890 (Leishmania mexicana)
Explore Q27890 
Go to UniProtKB:  Q27890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NBD
Query on NBD

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]N6-BENZYL-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C28 H33 N7 O14 P2
PDNSIRRMIDXSBH-INGGVVRRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.33α = 90
b = 125.81β = 90
c = 137.79γ = 90
Software Package:
Software NamePurpose
RAVEmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RAVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1999-03-05 
  • Released Date: 1999-03-16 
  • Deposition Author(s): Suresh, S., Hol, W.

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-16
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance