SMTL ID : 4ajp.1

Human LDHA in complex with 2-((4-(4-((3-((2-methyl-1,3-benzothiazol- 6yl)amino)-3-oxo-propyl)amino)-4-oxo-butyl)phenyl)methyl)propanedioic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-tetramer

Ligands

4 x 88N: {4-[4-({3-[(2-METHYL-1,3-BENZOTHIAZOL-6-YL)AMINO]-3-OXOPROPYL}AMINO)-4-OXOBUTYL]BENZYL}PROPANEDIOIC ACID(Non-covalent)

88N.1: 21 residues within 4Å: Chain A: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, Q.99, R.105, I.115, F.118, I.119, V.135, N.137, L.164, R.168, H.192, A.237, T.247, I.251 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.30, A:V.52, A:V.52, A:A.95, A:F.118, A:I.119, A:I.251 Hydrogen bonds: A:D.51, A:G.96, A:G.96, A:Q.99, A:N.137, A:T.247 Water bridges: A:V.30, A:G.31, A:N.137 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 88N.7: 21 residues within 4Å: Chain B: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, Q.99, R.105, I.115, F.118, I.119, V.135, N.137, L.164, R.168, H.192, A.237, T.247, I.251 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:V.30, B:A.95, B:F.118, B:I.119, B:I.251 Hydrogen bonds: B:D.51, B:G.96, B:G.96, B:Q.99, B:N.137 Water bridges: B:V.30, B:G.31, B:N.137, B:T.247 Salt bridges: B:R.105, B:R.105, B:R.168, B:H.192, B:H.192 88N.13: 21 residues within 4Å: Chain C: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, Q.99, R.105, I.115, F.118, I.119, V.135, N.137, L.164, R.168, H.192, A.237, T.247, I.251 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:V.30, C:V.52, C:A.95, C:F.118, C:I.251 Hydrogen bonds: C:D.51, C:G.96, C:G.96, C:Q.99, C:N.137, C:T.247 Water bridges: C:V.30, C:G.31, C:N.137 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 88N.16: 21 residues within 4Å: Chain D: G.26, G.28, V.30, D.51, V.52, T.94, A.95, G.96, Q.99, R.105, I.115, F.118, I.119, V.135, N.137, L.164, R.168, H.192, A.237, T.247, I.251 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:V.30, D:A.95, D:F.118, D:I.251 Hydrogen bonds: D:D.51, D:G.96, D:G.96, D:Q.99, D:N.137 Water bridges: D:V.30, D:G.31, D:N.137, D:H.192, D:T.247 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192

11 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.170, H.185, W.187 Chain C: S.183, H.185 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Water bridges: A:R.170, A:W.187, A:W.187, C:H.185 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.3: 4 residues within 4Å: Chain A: W.147, F.152, P.153, K.154 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.147, A:K.154 Water bridges: A:N.155 Salt bridges: A:K.154 SO4.4: 1 residues within 4Å: Chain A: K.148 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.148 SO4.5: 2 residues within 4Å: Chain A: N.83, Y.126 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.83 Salt bridges: A:K.125 SO4.8: 4 residues within 4Å: Chain B: R.170, H.185 Chain D: S.183, H.185 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Water bridges: D:A.206, B:H.185 Salt bridges: D:H.185, B:R.170, B:H.185 SO4.9: 4 residues within 4Å: Chain B: W.147, F.152, P.153, K.154 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.154 Water bridges: B:N.155 Salt bridges: B:K.154 SO4.10: 3 residues within 4Å: Chain B: T.219, D.220, K.221 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.220, B:D.220, B:K.221 SO4.14: 6 residues within 4Å: Chain A: L.182, S.183, H.185 Chain C: R.170, H.185, W.187 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Salt bridges: A:H.185, C:R.170, C:H.185 Water bridges: C:R.170, C:H.185 SO4.15: 4 residues within 4Å: Chain C: W.147, F.152, P.153, K.154 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.147, C:K.154 Salt bridges: C:K.154 SO4.17: 6 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185, W.187 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Water bridges: B:A.206 Salt bridges: B:H.185, D:R.170, D:H.185 Hydrogen bonds: D:W.187 SO4.18: 4 residues within 4Å: Chain D: W.147, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:F.152, D:K.154

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain B: G.28, A.29, R.98 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.29, B:R.98 GOL.11: 13 residues within 4Å: Chain A: S.201, G.202, M.203, N.204, G.207, S.209 Chain C: S.201, G.202, M.203, N.204, G.207, V.208, S.209 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:M.203, A:N.204, C:G.202 Water bridges: C:L.210 GOL.12: 3 residues within 4Å: Chain C: P.153, N.155, R.156 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.155, C:R.156, C:R.156

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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