Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 35.82 kDa 
• Atom Count: 2760 
• Modelled Residue Count: 315 
• Deposited Residue Count: 322 
• Unique protein chains: 1

1T2D

Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and oxalate

• PDB DOI: 10.2210/pdb1T2D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-04-21 Released: 2004-05-11 
• Deposition Author(s): Cameron, A., Read, J., Tranter, R., Winter, V.J., Sessions, R.B., Brady, R.L., Vivas, L., Easton, A., Kendrick, H., Croft, S.L., Barros, D., Lavandera, J.L., Martin, J.J., Risco, F., Garcia-Ochoa, S., Gamo, F.J., Sanz, L., Leon, L., Ruiz, J.R., Gabarro, R., Mallo, A., De Las Heras, F.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.152 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 

Literature

Identification and Activity of a Series of Azole-based Compounds with Lactate Dehydrogenase-directed Anti-malarial Activity.

Cameron, A., Read, J., Tranter, R., Winter, V.J., Sessions, R.B., Brady, R.L., Vivas, L., Easton, A., Kendrick, H., Croft, S.L., Barros, D., Lavandera, J.L., Martin, J.J., Risco, F., Garcia-Ochoa, S., Gamo, F.J., Sanz, L., Leon, L., Ruiz, J.R., Gabarro, R., Mallo, A., De Las Heras, F.G.

(2004) J Biol Chem 279: 31429-31439

• PubMed: 15117937 
• DOI: 10.1074/jbc.M402433200
• Primary Citation of Related Structures:  
  1T24, 1T25, 1T26, 1T2C, 1T2D, 1T2E, 1T2F


• PubMed Abstract: 
  

Plasmodium falciparum, the causative agent of malaria, relies extensively on glycolysis coupled with homolactic fermentation during its blood-borne stages for energy production. Selective inhibitors of the parasite lactate dehydrogenase (LDH), central to NAD(+) regeneration, therefore potentially provide a route to new antimalarial drugs directed against a novel molecular target. A series of heterocyclic, azole-based compounds are described that preferentially inhibit P. falciparum LDH at sub-micromolar concentrations, typically at concentrations about 100-fold lower than required for human lactate dehydrogenase inhibition. Crystal structures show these competitive inhibitors form a network of interactions with amino acids within the active site of the enzyme, stacking alongside the nicotinamide ring of the NAD(+) cofactor. These compounds display modest activity against parasitized erythrocytes, including parasite strains with known resistance to existing anti-malarials and against Plasmodium berghei in BALB/c mice. Initial toxicity data suggest the azole derivatives have generally low cytotoxicity, and preliminary pharmoco-kinetic data show favorable bioavailability and circulation times. These encouraging results suggest that further enhancement of these structures may yield candidates suitable for consideration as new therapeutics for the treatment of malaria. In combination these studies also provide strong support for the validity of targeting the Plasmodium glycolytic pathway and, in particular, LDH in the search for novel anti-malarials.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Recognition Centre, University of Bristol, Bristol BS8 1TD, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A	322	Plasmodium falciparum	Mutation(s): 0  Gene Names: LDH EC: 1.1.1.27
UniProt
Find proteins for Q27743 (Plasmodium falciparum (isolate CDC / Honduras)) Explore Q27743  Go to UniProtKB:  Q27743

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL	B [auth A]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.152 
• R-Value Work: 0.143 
• R-Value Observed: 0.143 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.507	α = 90
b = 86.583	β = 90
c = 90.339	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-21 
• Released Date: 2004-05-11 
Deposition Author(s): Cameron, A., Read, J., Tranter, R., Winter, V.J., Sessions, R.B., Brady, R.L., Vivas, L., Easton, A., Kendrick, H., Croft, S.L., Barros, D., Lavandera, J.L., Martin, J.J., Risco, F., Garcia-Ochoa, S., Gamo, F.J., Sanz, L., Leon, L., Ruiz, J.R., Gabarro, R., Mallo, A., De Las Heras, F.G.

Revision History  

• Version 1.0: 2004-05-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance