SMTL ID : 9bk3.1

Crystal structure of Lactate dehydrogenase in complex with 4-((4-(1-methyl-1H-imidazole-2-carbonyl)phenyl)amino)-4-oxo-2-(4-(trifluoromethyl)phenyl)butanoic acid (R-enantiomer, orthorhombic P form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: N.158, H.213 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain C: S.187, R.191 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: H.206 Chain D: R.191, H.206 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain D: S.187, R.191 Ligand excluded by PLIP

3 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 6 residues within 4Å: Chain B: N.158, L.185, R.189, H.213, A.258, T.268 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:A.258 Hydrogen bonds: B:N.158, B:T.268 Salt bridges: B:R.189, B:H.213, B:H.213 MLI.4: 7 residues within 4Å: Chain C: R.126, N.158, L.185, R.189, H.213, A.258, T.268 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.158, C:T.268 Salt bridges: C:R.126, C:R.126, C:R.189, C:H.213 MLI.8: 8 residues within 4Å: Chain D: Q.120, R.126, N.158, L.185, R.189, H.213, A.258, T.268 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.158, D:T.268 Salt bridges: D:R.126, D:R.126, D:R.189, D:H.213, D:H.213

1 x 01: (2R)-4-[4-(1-methyl-1H-imidazole-2-carbonyl)anilino]-4-oxo-2-[4-(trifluoromethyl)phenyl]butanoic acid

01.7: 13 residues within 4Å: Chain D: V.71, D.72, V.73, K.101, D.102, Y.103, N.104, A.116, I.136, F.139, I.140, N.143, Y.147 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.139 Hydrogen bonds: D:D.102, D:Y.103, D:Y.103, D:N.104, D:N.104, D:N.143 Salt bridges: D:K.146 pi-Stacking: D:Y.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, H. et al., Synthesis and biological characterization of an orally bioavailable lactate dehydrogenase-A inhibitor against pancreatic cancer. Eur.J.Med.Chem. (2024)

Release Date

2024-07-10

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-lactate dehydrogenase A chain

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