Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 35.71 kDa 
• Atom Count: 2511 
• Modelled Residue Count: 305 
• Deposited Residue Count: 321 
• Unique protein chains: 1

1U5C

Plasmodium falciparum lactate dehydrogenase complexed with 3,7-dihydroxynaphthalene-2-carboxylic acid and NAD+

• DOI: 10.2210/pdb1U5C/pdb

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


• Deposited: 2004-07-27 Released: 2005-06-21 
• Deposition Author(s): Conners, R., Cameron, A., Read, J., Schambach, F., Sessions, R.B., Brady, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.239 
• R-Value Work: 0.154 
• R-Value Observed: 0.158 

Literature

Mapping the binding site for gossypol-like inhibitors of Plasmodium falciparum lactate dehydrogenase.

Conners, R., Schambach, F., Read, J., Cameron, A., Sessions, R.B., Vivas, L., Easton, A., Croft, S.L., Brady, R.L.

(2005) Mol Biochem Parasitol 142: 137-148

• PubMed: 15978953 
• DOI: 10.1016/j.molbiopara.2005.03.015
• Primary Citation of Related Structures:  
  1XIV, 1U4O, 1U5C, 1U5A, 1U4S


• PubMed Abstract: 
  

Gossypol is a di-sesquiterpene natural-product in the form of a functionalised binaphthyl and is isolated from cotton plants. The compound has long been known to exhibit anti-malarial and other biological activities. Previous studies have indicated that compounds of this type target Plasmodium falciparum lactate dehydrogenase (pfLDH), an essential enzyme for energy generation within the parasite. In this study, we report that simple naphthalene-based compounds, the core of the gossypol structure, exhibit weak inhibition of the parasite lactate dehydrogenase. Crystal structures of the complexes formed by binding of these naphthalene-based compounds to their target enzyme have been used to delineate the molecular features likely to form the gossypol binding site. Two modes of binding are observed: one overlapping the pyruvate but not the co-factor site, the other bridging the binding sites for the co-factor nicontinamide group and pyruvate substrate. This latter site encompasses molecular features unique to Plasmodium forms of LDH and is likely to represent the mode of binding for gossypol derivatives that show selectivity for the parasite enzymes. We also report a substrate analogue that unexpectedly binds within the adenine pocket of the co-factor groove. Although these core pharmacophore-like molecules only exhibit low levels of inhibitory activity, these molecular snapshots provide a rational basis for renewed structure-based development of naphthalene-based compounds as anti-malarial agents.

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Organizational Affiliation: 

Department of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase	A	321	Plasmodium falciparum	Mutation(s): 0  EC: 1.1.1.27
Find proteins for Q27743 (Plasmodium falciparum (isolate CDC / Honduras)) Explore Q27743  Go to UniProtKB:  Q27743

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
BIK	C [auth A]	3,7-DIHYDROXY-2-NAPHTHOIC ACID C11 H8 O4 QMWOUSYSNFCKAZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.239 
• R-Value Work: 0.154 
• R-Value Observed: 0.158 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.225	α = 90
b = 86.017	β = 90
c = 91.07	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: 2004-07-27 
• Released Date: 2005-06-21 
Deposition Author(s): Conners, R., Cameron, A., Read, J., Schambach, F., Sessions, R.B., Brady, R.L.

Revision History  

• Version 1.0: 2005-06-21
  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