ISDA

Deposition Date 2014-08-22

Release Date 2014-12-24

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4R69

Keywords:

OXIDOREDUCTASE

Title:

Lactate Dehydrogenase in complex with inhibitor compound 13

Biological Source:

Source Organism:

Homo sapiens (Taxon ID: 9606)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.19 Å

R-Value Free:

0.22

R-Value Work:

0.18

R-Value Observed:

0.19

Space Group:

P 1 21 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

NAI

SO4

W13

Primary Citation

Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase.

Labadie, S, Dragovich, P.S, Chen, J, Fauber, B.P, Boggs, J, Corson, L.B, Ding, C.Z, Eigenbrot, C, Ge, H, Ho, Q, Lai, K.W, Ma, S, Malek, S, Peterson, D, Purkey, H.E, Robarge, K, Salphati, L, Sideris, S, Ultsch, M, VanderPorten, E, Wei, B, Xu, Q, Yen, I, Yue, Q, Zhang, H, Zhang, X, Zhou, A.Show

Bioorg.Med.Chem.Lett. 25 75 82 (2014)

PMID: 25466195 DOI: 10.1016/j.bmcl.2014.11.008

Abstact

Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enone using structure-based design strategies resulted in inhibitors with considerable improvement in biochemical potency against human lactate dehydrogenase A (LDHA). These potent inhibitors were typically selective for LDHA over LDHB isoform (4–10 fold) and other structurally related malate dehydrogenases, MDH1 and MDH2 (>500 fold). An X-ray crystal structure of enzymatically most potent molecule bound to LDHA revealed two additional interactions associated with enhanced biochemical potency.

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Primary Citation of related structures