› 4jnk

X-ray diffraction
1.9Å resolution

Lactate Dehydrogenase A in complex with inhibitor compound 22

Released:
DOI: 10.2210/pdb4jnk/pdb
PDB entry 4jnk coloured by chain, front view.
PDB entry 4jnk coloured by chain, side view.
PDB entry 4jnk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of substituted 2-thio-6-oxo-1,6-dihydropyrimidines as inhibitors of human lactate dehydrogenase.
Dragovich PS, Fauber BP, Corson LB, Ding CZ, Eigenbrot C, Ge H, Giannetti AM, Hunsaker T, Labadie S, Liu Y, Malek S, Pan B, Peterson D, Pitts K, Purkey HE, Sideris S, Ultsch M, VanderPorten E, Wei B, Xu Q, Yen I, Yue Q, Zhang H, Zhang X
Bioorg Med Chem Lett 23 3186-94 (2013)
PMID: 23628333

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-132412 (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: 36.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P00338 (Residues: 2-332; Coverage: 100%)
Gene names: LDHA, PIG19
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAI 4 x NAI
4 bound ligands:
Ligand EPE 3 x EPE
Ligand ZHK 3 x ZHK
Ligand SO4 3 x SO4
Ligand LAC 1 x LAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: C2
Unit cell:
a: 168.246Å b: 81.487Å c: 120.414Å
α: 90° β: 117.13° γ: 90°
R-values:
R R work R free
0.161 0.159 0.204
Expression system: Escherichia coli

Quick links

Citations

6 review citations

An update on therapeutic opportunities offered by cancer glycolytic metabolism.
Granchi et al. (2014)
5 more

7 mentions without citation

Small-molecule inhibitors of human LDH5.
Granchi et al. (2013)
6 more