SMTL ID : 4ajl.1

rat LDHA in complex with 3-(ethylcarbamoylamino)-N-(2-methyl-1,3- benzothiazol-6-yl)propanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-tetramer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: S.201, G.202, V.203, N.204, G.207, S.209 Chain D: S.201, G.202, N.204, G.207, S.209 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.202, D:N.204, D:G.207, A:V.203 Water bridges: A:L.210 GOL.5: 7 residues within 4Å: Chain A: M.40, K.41 Chain B: M.40, D.42, F.70, L.71, K.72 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.42, B:K.72, A:M.40 Water bridges: B:L.39, B:D.42 GOL.9: 11 residues within 4Å: Chain C: N.163, S.166, A.167, R.170, W.187, V.269, H.270, P.271 Chain D: L.69, F.70 Ligands: MLI.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.170, C:V.269, C:H.270 Water bridges: C:S.166, C:S.166, C:G.186, C:W.187 GOL.11: 11 residues within 4Å: Chain B: S.201, G.202, N.204, G.207, S.209 Chain C: S.201, G.202, V.203, N.204, G.207, S.209 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.201, B:S.201, B:N.204 Water bridges: C:L.210 GOL.12: 4 residues within 4Å: Chain C: S.104, L.106, N.107, I.325 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.104, C:N.107 Water bridges: C:D.194, C:D.194 GOL.16: 7 residues within 4Å: Chain C: M.40, K.41 Chain D: M.40, D.42, F.70, L.71, K.72 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.42, C:M.40 Water bridges: D:D.42, D:D.42

4 x 88W: N~3~-(ethylcarbamoyl)-N-(2-methyl-1,3-benzothiazol-6-yl)-beta-alaninamide

88W.2: 12 residues within 4Å: Chain A: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.30, A:V.52, A:A.95, A:F.118 Hydrogen bonds: A:D.51, A:G.96, A:G.96, A:G.96 Water bridges: A:A.29, A:V.30, A:V.30, A:Y.82, A:T.94, A:T.94, A:N.112 88W.6: 13 residues within 4Å: Chain B: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119, S.136 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.95, B:F.118, B:I.119 Hydrogen bonds: B:D.51, B:G.96, B:G.96, B:G.96, B:R.98 Water bridges: B:G.28, B:A.29, B:Y.82 88W.13: 11 residues within 4Å: Chain C: G.26, G.28, D.51, V.52, T.94, A.95, G.96, I.115, F.118, I.119 Ligands: DMS.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.52, C:A.95, C:F.118, C:I.119 Hydrogen bonds: C:D.51, C:G.96, C:G.96, C:G.96 Water bridges: C:G.28, C:A.29, C:A.29, C:N.112 88W.17: 11 residues within 4Å: Chain D: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.52, D:A.95, D:F.118, D:I.119 Hydrogen bonds: D:D.51, D:G.96, D:G.96, D:G.96 Water bridges: D:G.28, D:G.28, D:A.29, D:V.30, D:N.112

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

MLI.3: 8 residues within 4Å: Chain A: R.105, N.137, L.164, R.168, H.192, A.237, T.247, I.251 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251 Hydrogen bonds: A:N.137, A:T.247, A:T.247 Water bridges: A:T.247 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 MLI.4: 6 residues within 4Å: Chain A: R.170, H.185, W.187, V.269 Chain D: S.183, H.185 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain A Water bridges: D:L.182, D:S.183, D:A.206, A:R.170, A:V.269 Salt bridges: D:H.185, D:H.185, A:R.170, A:H.185 MLI.7: 6 residues within 4Å: Chain B: R.170, H.185, W.187, V.269 Chain C: S.183, H.185 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Water bridges: B:R.170, B:V.269, C:L.182, C:S.183, C:A.206 Salt bridges: B:R.170, B:H.185, C:H.185, C:H.185 MLI.8: 8 residues within 4Å: Chain B: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.99, B:N.137, B:T.247, B:T.247 Water bridges: B:T.247 Salt bridges: B:R.105, B:R.105, B:R.168, B:H.192, B:H.192 MLI.14: 8 residues within 4Å: Chain C: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.99, C:N.137, C:T.247 Water bridges: C:T.247, C:T.247 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 MLI.15: 7 residues within 4Å: Chain B: S.183, H.185 Chain C: R.170, H.185, W.187, V.269 Ligands: GOL.9 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Water bridges: B:L.182, B:S.183, B:S.183, C:R.170, C:H.185, C:V.269 Salt bridges: B:H.185, B:H.185, C:R.170, C:H.185 MLI.18: 8 residues within 4Å: Chain D: R.105, N.137, L.164, R.168, H.192, A.237, T.247, I.251 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251 Hydrogen bonds: D:N.137, D:T.247 Water bridges: D:R.168, D:T.247 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192 MLI.19: 6 residues within 4Å: Chain A: S.183, H.185 Chain D: R.170, H.185, W.187, V.269 9 PLIP interactions: 4 interactions with chain A, 5 interactions with chain D Water bridges: A:L.182, A:S.183, D:R.170, D:H.185, D:V.269 Salt bridges: A:H.185, A:H.185, D:R.170, D:H.185

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

DMS.10: 4 residues within 4Å: Chain C: G.96, A.97, I.115 Ligands: 88W.13 No protein-ligand interaction detected (PLIP)

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

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