SMTL ID : 4aj4.1

rat LDHA in complex with 4-((2-allylsulfanyl-1,3-benzothizol-6-yl) amino)-4-oxo-butanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

MLI.1: 8 residues within 4Å: Chain A: R.106, N.138, L.165, R.169, H.193, A.238, T.248, I.252 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.165, A:I.252 Hydrogen bonds: A:N.138, A:T.248 Water bridges: A:T.248 Salt bridges: A:R.106, A:R.106, A:R.169, A:H.193, A:H.193 MLI.3: 6 residues within 4Å: Chain A: R.171, H.186, W.188, V.270 Chain D: S.184, H.186 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Water bridges: D:L.183, D:S.184, D:A.207, A:R.171 Salt bridges: D:H.186, D:H.186, A:R.171, A:H.186 Hydrogen bonds: A:V.270 MLI.4: 6 residues within 4Å: Chain B: R.171, H.186, W.188, V.270 Chain C: S.184, H.186 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:V.270 Water bridges: B:R.171, C:L.183, C:A.207 Salt bridges: B:R.171, B:H.186, C:H.186, C:H.186 MLI.6: 8 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.100, B:N.138, B:T.248, B:T.248 Water bridges: B:T.248 Salt bridges: B:R.106, B:R.106, B:R.169, B:H.193, B:H.193 MLI.7: 8 residues within 4Å: Chain C: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.100, C:N.138, C:T.248 Water bridges: C:T.248, C:T.248, C:I.252 Salt bridges: C:R.106, C:R.106, C:R.169, C:H.193, C:H.193 MLI.8: 6 residues within 4Å: Chain B: S.184, H.186 Chain C: R.171, H.186, W.188, V.270 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Water bridges: C:R.171, C:H.186, C:V.270, C:V.270 Salt bridges: C:R.171, C:H.186, B:H.186, B:H.186 MLI.10: 7 residues within 4Å: Chain D: R.106, N.138, L.165, R.169, H.193, A.238, T.248 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.165 Hydrogen bonds: D:N.138, D:T.248 Water bridges: D:T.248 Salt bridges: D:R.106, D:R.106, D:R.169, D:H.193, D:H.193 MLI.11: 7 residues within 4Å: Chain A: L.183, S.184, H.186 Chain D: R.171, H.186, W.188, V.270 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Water bridges: D:R.171, D:H.186 Salt bridges: D:R.171, D:H.186, A:H.186, A:H.186

4 x VAB: 4-oxo-4-{[2-(prop-2-en-1-ylsulfanyl)-1,3-benzothiazol-6-yl]amino}butanoic acid(Non-covalent)

VAB.2: 9 residues within 4Å: Chain A: G.27, G.29, D.52, V.53, A.96, G.97, I.116, F.119, I.120 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.53, A:A.96 Hydrogen bonds: A:D.52, A:G.97 Water bridges: A:G.29, A:G.29, A:A.30, A:T.95, A:G.97, A:R.99 Salt bridges: A:R.99 VAB.5: 10 residues within 4Å: Chain B: G.27, G.29, D.52, V.53, A.96, G.97, R.99, I.116, F.119, I.120 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.53, B:A.96, B:F.119, B:I.120 Hydrogen bonds: B:D.52, B:G.97 Water bridges: B:A.30, B:Y.83, B:R.99 Salt bridges: B:R.99 VAB.9: 12 residues within 4Å: Chain C: G.27, G.29, D.52, V.53, T.95, A.96, G.97, R.99, N.115, I.116, F.119, I.120 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.96 Hydrogen bonds: C:D.52, C:T.95, C:G.97 Water bridges: C:A.30, C:A.30 Salt bridges: C:R.99 VAB.12: 9 residues within 4Å: Chain D: G.27, G.29, D.52, V.53, A.96, G.97, I.116, F.119, I.120 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:D.52, D:V.53, D:A.96 Hydrogen bonds: D:D.52, D:G.97 Water bridges: D:A.30, D:A.30, D:A.30 Salt bridges: D:R.99

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ward, R. et al., The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation. J.Med.Chem. (2012)

Release Date

2012-03-21

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