ISDA: 4JNK

Deposition Date 2013-03-15

Release Date 2013-05-22

Last Version Date 2023-11-15

Entry Detail

PDB ID:

4JNK

Keywords:

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR

Title:

Lactate Dehydrogenase A in complex with inhibitor compound 22

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.90 Å

R-Value Free:

0.20

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

C 1 2 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:L-lactate dehydrogenase A chain
Gene (Uniprot):LDHA
Chain IDs:A, B, C, D
Chain Length:331
Number of Molecules:4
Biological Source:Homo sapiens

UniProt ID:P00338 Pfam ID:PF00056, PF02866 EC:1.1.1.27

Ligand Molecules

EPE

LAC

NAI

SO4

ZHK

Primary Citation

Identification of substituted 2-thio-6-oxo-1,6-dihydropyrimidines as inhibitors of human lactate dehydrogenase.

Dragovich, P.S, Fauber, B.P, Corson, L.B, Ding, C.Z, Eigenbrot, C, Ge, H, Giannetti, A.M, Hunsaker, T, Labadie, S, Liu, Y, Malek, S, Pan, B, Peterson, D, Pitts, K, Purkey, H.E, Sideris, S, Ultsch, M, Vanderporten, E, Wei, B, Xu, Q, Yen, I, Yue, Q, Zhang, H, Zhang, X.Show

Bioorg.Med.Chem.Lett. 23 3186 3194 (2013)

PMID: 23628333 DOI: 10.1016/j.bmcl.2013.04.001

Abstact

A novel 2-thio-6-oxo-1,6-dihydropyrimidine-containing inhibitor of human lactate dehydrogenase (LDH) was identified by high-throughput screening (IC50=8.1 μM). Biochemical, surface plasmon resonance, and saturation transfer difference NMR experiments indicated that the compound specifically associated with human LDHA in a manner that required simultaneous binding of the NADH co-factor. Structural variation of the screening hit resulted in significant improvements in LDHA biochemical inhibition activity (best IC50=0.48 μM). A crystal structure of an optimized compound bound to human LDHA was obtained and explained many of the observed structure-activity relationships.

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Primary Citation of related structures