SMTL ID : 4aj1.1

rat LDHA in complex with N-(2-(methylamino)-1,3-benzothiazol-6-yl) acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: L.39, D.42, F.70, L.71, K.72 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:L.39, A:K.72, A:K.72 Water bridges: A:M.40, A:D.42, A:K.72, B:K.41 GOL.5: 11 residues within 4Å: Chain B: S.201, G.202, V.203, N.204, G.207, S.209 Chain C: S.201, G.202, N.204, G.207, S.209 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:V.203, C:G.202, C:N.204, C:G.207 Water bridges: B:L.210 GOL.9: 2 residues within 4Å: Chain C: S.104, N.107 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.104, C:N.107 Water bridges: C:D.194 GOL.14: 7 residues within 4Å: Chain C: M.40, K.41 Chain D: M.40, D.42, F.70, L.71, K.72 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:F.70, C:M.40 Water bridges: D:D.42

4 x AJ1: N-(2-METHYLAMINO)-1,3-BENZOTHIAZOL-6-YL)ACETAMIDE(Non-covalent)

AJ1.2: 9 residues within 4Å: Chain A: G.26, G.28, D.51, V.52, A.95, G.96, I.115, F.118, I.119 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.52, A:A.95 Hydrogen bonds: A:D.51, A:G.96 AJ1.6: 9 residues within 4Å: Chain B: G.26, G.28, D.51, V.52, A.95, G.96, I.115, F.118, I.119 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.52, B:A.95 Hydrogen bonds: B:D.51, B:G.96 Water bridges: B:Y.82 AJ1.10: 9 residues within 4Å: Chain C: G.28, D.51, V.52, A.95, G.96, R.98, I.115, F.118, I.119 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:V.52, C:A.95, C:I.119 Hydrogen bonds: C:D.51, C:G.96 AJ1.15: 9 residues within 4Å: Chain D: G.26, G.28, D.51, V.52, A.95, G.96, I.115, F.118, I.119 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:D.51, D:V.52, D:V.52, D:A.95 Hydrogen bonds: D:D.51, D:G.96

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 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251 Hydrogen bonds: A:N.137, 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 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain A Water bridges: D:S.183, D:H.185, D:A.206, A:R.170, A:R.170, A:W.187, 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 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:V.269 Water bridges: B:R.170, B:R.170, B:W.187, B:V.269, 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:N.137 Salt bridges: B:R.105, B:R.105, B:R.168, B:H.192, B:H.192 MLI.11: 8 residues within 4Å: Chain C: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.99, C:N.137, C:T.247 Water bridges: C:N.137, C:T.247, C:T.247 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 MLI.12: 7 residues within 4Å: Chain B: L.182, S.183, H.185 Chain C: R.170, H.185, W.187, V.269 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Water bridges: C:R.170, C:R.170, C:H.185, C:W.187, C:V.269, B:S.183 Salt bridges: C:R.170, C:H.185, B:H.185, B:H.185 MLI.16: 7 residues within 4Å: Chain D: R.105, N.137, L.164, R.168, H.192, A.237, T.247 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.164 Hydrogen bonds: D:N.137, D:T.247 Water bridges: D:T.247 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192 MLI.17: 7 residues within 4Å: Chain A: L.182, S.183, H.185 Chain D: R.170, H.185, W.187, V.269 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain D Water bridges: A:S.183, D:R.170, D:R.170, D:H.185, D:W.187, D:V.269 Salt bridges: A:H.185, A:H.185, D:R.170, D:H.185 Hydrophobic interactions: D:W.187

1 x OXM: OXAMIC ACID(Non-covalent)

OXM.13: 9 residues within 4Å: Chain A: S.201, G.202, N.204, G.207 Chain D: S.201, G.202, N.204, G.207, S.209 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.204, A:S.209, D:N.204, D:G.207

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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