SMTL ID : 4r68.1

Lactate Dehydrogenase in complex with inhibitor compound 31

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-tetramer

Ligands

4 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.1: 24 residues within 4Å: Chain A: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: W31.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:V.135, A:L.164, A:I.251 Hydrogen bonds: A:V.30, A:V.52, A:Y.82, A:G.96, A:V.135, A:N.137, A:N.137 Water bridges: A:G.28, A:A.29, A:G.31, A:G.96, A:A.97, A:R.98, A:N.112 Salt bridges: A:R.98 NAI.4: 24 residues within 4Å: Chain B: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: W31.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:V.135, B:I.251 Hydrogen bonds: B:G.28, B:A.29, B:V.30, B:V.52, B:G.96, B:V.135, B:N.137, B:N.137 Water bridges: B:G.31, B:R.98, B:R.98, B:R.98, B:R.98, B:R.98, B:N.112 Salt bridges: B:R.98 NAI.7: 23 residues within 4Å: Chain C: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: W31.9 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.164, C:T.247, C:I.251, C:I.251 Hydrogen bonds: C:G.28, C:A.29, C:V.30, C:V.52, C:G.96, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.31 NAI.10: 23 residues within 4Å: Chain D: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, I.115, F.118, I.119, V.135, S.136, N.137, V.139, L.164, H.192, T.247, I.251 Ligands: W31.11 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:V.52, D:G.96, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31, D:Q.99, D:N.112, D:N.112

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: W.147, G.151, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.154 EPE.5: 5 residues within 4Å: Chain B: W.147, G.151, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.154 EPE.8: 5 residues within 4Å: Chain C: W.147, G.151, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.154 EPE.12: 4 residues within 4Å: Chain D: A.97, R.98, E.103, R.111 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.98 Salt bridges: D:E.103, D:E.103, D:R.111

4 x W31: (1S)-1-phenylethyl (4-chloro-3-{[(4S)-4-(2,6-dichlorophenyl)-2-hydroxy-6-oxocyclohex-1-en-1-yl]sulfanyl}phenyl)acetate(Non-covalent)

W31.3: 16 residues within 4Å: Chain A: R.105, L.108, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.233, V.234, A.237, Y.238, I.241, T.247 Ligands: NAI.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.105, A:L.108, A:N.137, A:V.234, A:A.237, A:Y.238, A:I.241, A:T.247 Hydrogen bonds: A:N.137, A:R.168, A:R.168, A:H.192, A:D.194 Water bridges: A:R.105 Salt bridges: A:R.105 pi-Cation interactions: A:R.105 W31.6: 16 residues within 4Å: Chain B: R.105, L.108, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.233, V.234, A.237, Y.238, I.241, T.247 Ligands: NAI.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.108, B:A.237, B:Y.238, B:T.247 Hydrogen bonds: B:N.137, B:R.168, B:R.168, B:H.192, B:D.194, B:T.247 Water bridges: B:R.105 Salt bridges: B:R.105 pi-Cation interactions: B:R.105 W31.9: 13 residues within 4Å: Chain C: N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, T.247 Ligands: NAI.7 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:N.137, C:V.234, C:A.237, C:Y.238, C:T.247 Hydrogen bonds: C:N.137, C:R.168, C:R.168, C:H.192, C:D.194, C:Y.238 Water bridges: C:D.194 W31.11: 15 residues within 4Å: Chain D: Q.99, L.108, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.233, A.237, Y.238, I.241, T.247 Ligands: NAI.10 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.108, D:N.137, D:A.237, D:Y.238, D:I.241, D:T.247 Hydrogen bonds: D:N.137, D:R.168, D:R.168, D:H.192, D:D.194, D:Y.238, D:T.247

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

SO4.13: 5 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain D Water bridges: B:A.206, D:R.170, D:R.170, D:R.170, D:V.269, D:V.269 Salt bridges: B:H.185, D:R.170, D:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Labadie, S. et al., Optimization of 5-(2,6-dichlorophenyl)-3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-12-24

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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