SMTL ID : 4r69.1

Lactate Dehydrogenase in complex with inhibitor compound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

homo-tetramer

Ligands

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

EPE.1: 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.4: 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.7: 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

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

NAI.2: 27 residues within 4Å: Chain A: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, A.97, R.98, N.112, I.115, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: W13.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.164, A:T.247, A:I.251, A:I.251 Hydrogen bonds: A:A.29, A:V.30, A:V.52, A:Y.82, A:G.96, A:R.98, A:R.98, A:N.112, A:N.137, A:N.137, A:S.160, A:S.160 Salt bridges: A:R.98, A:R.98 NAI.5: 28 residues within 4Å: Chain B: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, K.56, Y.82, T.94, A.95, G.96, A.97, 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: W13.6 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.164, B:I.251, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:K.56, B:G.96, B:A.97, B:R.98, B:N.137, B:N.137, B:S.160, B:S.160 Salt bridges: B:R.98, B:R.98 NAI.8: 27 residues within 4Å: Chain C: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, A.97, 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: W13.9 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.164, C:T.247, C:I.251, C:I.251 Hydrogen bonds: C:A.29, C:V.30, C:V.52, C:G.96, C:R.98, C:N.137, C:N.137, C:S.160, C:S.160 Salt bridges: C:R.98, C:R.98 NAI.10: 27 residues within 4Å: Chain D: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, A.97, 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: W13.12 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251, D:I.251 Hydrogen bonds: D:A.29, D:V.30, D:V.52, D:G.96, D:G.96, D:R.98, D:N.112, D:N.137, D:N.137, D:S.160, D:S.160 Salt bridges: D:R.98, D:R.98

4 x W13: (5R)-2-[(2-chlorophenyl)sulfanyl]-5-[2,6-dichloro-3-(tetrahydro-2H-pyran-4-ylamino)phenyl]-3-hydroxycyclohex-2-en-1-one(Non-covalent)

W13.3: 16 residues within 4Å: Chain A: R.98, Q.99, 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.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.98, A:Q.99, A:A.237, A:Y.238, A:I.241, A:I.241, A:T.247 Hydrogen bonds: A:N.137, A:R.168, A:R.168 W13.6: 15 residues within 4Å: Chain B: R.98, 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.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.98, B:V.234, B:A.237, B:Y.238, B:I.241, B:I.241, B:T.247 Hydrogen bonds: B:N.137, B:R.168, B:R.168, B:T.247 W13.9: 16 residues within 4Å: Chain C: R.98, G.102, E.103, 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.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:R.98, C:V.234, C:A.237, C:Y.238, C:I.241, C:I.241, C:T.247 Hydrogen bonds: C:N.137, C:R.168, C:R.168 W13.12: 16 residues within 4Å: Chain D: R.98, Q.99, 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.10 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:R.98, D:V.234, D:A.237, D:Y.238, D:I.241, D:T.247 Hydrogen bonds: D:N.137, D:R.168, D:R.168, D:T.247

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

SO4.11: 5 residues within 4Å: Chain B: S.183, H.185 Chain D: R.170, H.185, W.187 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.170, D:H.185, B: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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