SMTL ID : 4ajh.1

rat LDHA in complex with N-(2-methyl-1,3-benzothiazol-6-yl)-3-ureido- propanamide and 2-(4-bromophenoxy)propanedioic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

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

MLI.1: 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.2: 6 residues within 4Å: Chain A: R.170, H.185, W.187, V.269 Chain D: S.183, H.185 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain D Water bridges: A:R.170, A:V.269, D:L.182, D:S.183, D:S.183, D:A.206 Salt bridges: A:R.170, A:H.185, D:H.185, D:H.185 MLI.4: 6 residues within 4Å: Chain B: R.170, H.185, W.187, V.269 Chain C: S.183, H.185 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Water bridges: C:S.183, C:A.206, B:R.170, B:V.269 Salt bridges: C:H.185, C:H.185, B:R.170, B:H.185 MLI.8: 6 residues within 4Å: Chain B: S.183, H.185 Chain C: R.170, H.185, W.187, V.269 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B Water bridges: C:R.170, C:H.185, C:V.269, B:L.182, B:S.183 Salt bridges: C:R.170, C:H.185, B:H.185, B:H.185 MLI.11: 9 residues within 4Å: Chain C: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: 2B4.10 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:Q.99, C:N.137 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.13: 7 residues within 4Å: Chain D: R.105, N.137, L.164, R.168, H.192, A.237, T.247 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.164 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.14: 6 residues within 4Å: Chain A: S.183, H.185 Chain D: R.170, H.185, W.187, V.269 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain A Water bridges: D:R.170, D:V.269, A:L.182, A:L.182, A:S.183, A:S.183, A:A.206 Salt bridges: D:R.170, D:H.185, A:H.185, A:H.185

4 x 88S: N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)-3-UREIDO-PROPANAMIDE(Non-covalent)

88S.3: 11 residues within 4Å: Chain A: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.52, 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:G.28, A:A.29, A:V.30 88S.5: 12 residues within 4Å: Chain B: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 Ligands: 2B4.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:V.52, B:V.52, B:A.95, B:F.118, B:I.119 Hydrogen bonds: B:G.28, B:D.51, B:G.96, B:G.96, B:G.96 Water bridges: B:A.29, B:V.30, B:V.30, B:Y.82, B:R.98, B:R.98 88S.9: 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: 2B4.10 11 PLIP interactions: 11 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:V.30 88S.15: 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 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:V.52, D:V.52, D:A.95, D:F.118, D:I.119 Hydrogen bonds: D:G.28, D:D.51, D:G.96, D:G.96, D:G.96 Water bridges: D:A.29, D:V.30, D:G.31, D:N.112

2 x 2B4: 2-(4-BROMANYLPHENOXY)PROPANEDIOIC ACID(Non-covalent)

2B4.6: 14 residues within 4Å: Chain B: V.30, T.94, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247, I.251 Ligands: 88S.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.30, B:V.135, B:I.251 Hydrogen bonds: B:Q.99, B:N.137, 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 Halogen bonds: B:T.94 2B4.10: 15 residues within 4Å: Chain C: V.30, T.94, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247, I.251 Ligands: 88S.9, MLI.11 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:V.30, C:V.30, C:V.135, C:I.251 Hydrogen bonds: C:Q.99, C:N.137 Water bridges: C:T.247, C:I.251 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 Halogen bonds: C:T.94

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain B: S.201, G.202, N.204, G.207 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:G.202, B:G.202, B:N.204 Water bridges: C:L.210 GOL.12: 7 residues within 4Å: Chain C: K.41 Chain D: L.39, M.40, D.42, F.70, L.71, K.72 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.72 Water bridges: D:L.39, D:D.42

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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