› 4aji

X-ray diffraction
1.93Å resolution

rat LDHA in complex with 2-((3,4-dimethoxyphenyl)methyl))propanedioic acid

Released:
DOI: 10.2210/pdb4aji/pdb
PDB entry 4aji coloured by chain, front view.
PDB entry 4aji coloured by chain, side view.
PDB entry 4aji coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Design and synthesis of novel lactate dehydrogenase A inhibitors by fragment-based lead generation.
Ward RA, Brassington C, Breeze AL, Caputo A, Critchlow S, Davies G, Goodwin L, Hassall G, Greenwood R, Holdgate GA, Mrosek M, Norman RA, Pearson S, Tart J, Tucker JA, Vogtherr M, Whittaker D, Wingfield J, Winter J, Hudson K
J Med Chem 55 3285-306 (2012)
PMID: 22417091

Function and Biology Details

Reaction catalysed: 
(S)-lactate + NAD(+) = pyruvate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138140 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-lactate dehydrogenase A chain Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 331 amino acids
Theoretical weight: 36.36 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P04642 (Residues: 2-332; Coverage: 100%)
Gene names: Ldh-1, Ldh1, Ldha
Sequence domains:
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 88R 4 x 88R
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P21
Unit cell:
a: 61.923Å b: 81.649Å c: 128.994Å
α: 90° β: 96.08° γ: 90°
R-values:
R R work R free
0.164 0.162 0.198
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

19 review citations

Twenty years on: the impact of fragments on drug discovery.
Erlanson et al. (2016)
18 more

1 mention without citation

Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A.
Lukac et al. (2019)