SMTL ID : 9bk2.1

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 (S-enantiomer, monoclinic P form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 6 residues within 4Å: Chain A: N.184, S.187, R.191, V.290, P.292 Chain C: L.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.191 pi-Cation interactions: A:W.208 DMS.5: 7 residues within 4Å: Chain B: N.184, S.187, R.191, W.208, V.290, P.292 Chain D: L.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.191 pi-Cation interactions: B:W.208 DMS.9: 7 residues within 4Å: Chain A: L.90 Chain C: N.184, S.187, R.191, V.290, P.292 Ligands: MLI.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.191 DMS.13: 6 residues within 4Å: Chain B: L.90 Chain D: N.184, S.187, R.191, V.290, P.292 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.191 pi-Cation interactions: D:W.208

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

01.2: 14 residues within 4Å: Chain A: S.222, N.225, G.228, V.229, S.230, K.232, T.233, P.236 Chain D: S.222, G.223, N.225, G.228, S.230, T.233 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:T.233, A:S.230, A:T.233 Halogen bonds: D:G.223 Hydrophobic interactions: A:K.232 pi-Cation interactions: A:K.232

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

MLI.3: 6 residues within 4Å: Chain A: R.191, H.206, W.208, V.290 Chain D: S.204, H.206 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Water bridges: D:S.204, D:H.206, D:A.227, A:R.191, A:R.191, A:W.208, A:V.290 Salt bridges: D:H.206, D:H.206, A:R.191, A:H.206 MLI.4: 9 residues within 4Å: Chain A: R.119, Q.120, R.126, N.158, L.185, R.189, H.213, A.258, T.268 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.158, A:T.268 Water bridges: A:R.189 Salt bridges: A:R.119, A:R.126, A:R.126, A:R.189, A:H.213, A:H.213 MLI.6: 8 residues within 4Å: Chain B: R.126, N.158, L.185, R.189, H.213, A.258, T.268, I.272 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.185, B:I.272 Hydrogen bonds: B:N.158, B:T.268 Water bridges: B:T.268 Salt bridges: B:R.126, B:R.126, B:R.189, B:H.213, B:H.213 MLI.7: 6 residues within 4Å: Chain B: R.191, H.206, W.208, V.290 Chain C: S.204, H.206 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Water bridges: C:H.206, C:A.227, B:V.290 Salt bridges: C:H.206, C:H.206, B:R.191, B:H.206 Hydrophobic interactions: B:W.208 MLI.8: 7 residues within 4Å: Chain B: V.46, D.72, V.73, Y.103, A.116, I.136, I.140 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.73, B:I.140 Hydrogen bonds: B:D.72, B:Y.103 MLI.10: 8 residues within 4Å: Chain C: R.126, N.158, L.185, R.189, H.213, A.258, T.268, I.272 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.185, C:I.272 Hydrogen bonds: C:N.158, C:T.268 Water bridges: C:T.268 Salt bridges: C:R.126, C:R.126, C:R.189, C:H.213, C:H.213 MLI.11: 7 residues within 4Å: Chain B: S.204, H.206 Chain C: R.191, H.206, W.208, V.290 Ligands: DMS.9 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:W.208 Water bridges: C:V.290, B:A.227 Salt bridges: C:R.191, C:H.206, B:H.206, B:H.206 MLI.12: 9 residues within 4Å: Chain C: V.46, V.71, D.72, V.73, Y.103, A.116, I.136, F.139, I.140 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.73 Hydrogen bonds: C:G.47, C:D.72, C:Y.103 MLI.14: 7 residues within 4Å: Chain A: L.203, S.204, H.206 Chain D: R.191, H.206, W.208, V.290 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain A Water bridges: D:R.191, D:H.206, D:W.208, D:V.290, A:H.206 Salt bridges: D:R.191, D:H.206, A:H.206, A:H.206 MLI.15: 9 residues within 4Å: Chain D: R.119, R.126, N.158, L.185, R.189, H.213, A.258, T.268, I.272 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.185, D:I.272 Hydrogen bonds: D:N.158, D:T.268 Salt bridges: D:R.119, D:R.126, D:R.126, D:R.189, D:H.213, D:H.213

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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