SMTL ID : 4qo7.1

Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 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, A.97, R.98, I.115, I.119, V.135, S.136, N.137, V.139, L.164, H.192, T.247, I.251 Ligands: 36V.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.251, A:I.251 Hydrogen bonds: A:G.28, A:A.29, A:V.30, A:V.52, A:G.96, A:A.97, A:V.135, A:N.137, A:N.137 Water bridges: A:G.31, A:R.98, A:R.98 Salt bridges: A:R.98, A:R.98 NAI.4: 25 residues within 4Å: Chain B: G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, N.112, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: 2OP.5 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, B:G.96, B:A.97, B:N.112, B:V.135, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31, B:R.98, B:R.98, B:Q.99 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.7: 22 residues within 4Å: Chain C: 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, S.160, L.164, H.192, T.247, I.251 Ligands: 36V.9 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:V.135, C:L.164, C:I.251 Hydrogen bonds: 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.28, C:A.29, C:A.29, C:G.31, C:Y.82, C:R.98, C:R.98, C:R.98, C:R.98, C:N.137 Salt bridges: C:R.98 NAI.10: 24 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, 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: 36V.11 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251 Hydrogen bonds: D:G.28, D:V.30, D:V.52, D:G.96, D:V.135, D:N.137, D:N.137 Water bridges: D:A.29, D:A.29, D:G.31, D:Y.82, D:T.94, D:G.96, D:A.97 Salt bridges: D:R.98

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

EPE.2: 4 residues within 4Å: Chain A: W.147, G.151, P.153, K.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.147, A:K.154 EPE.6: 5 residues within 4Å: Chain B: W.147, G.151, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.147, 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

3 x 36V: trans-2-[(2-nitrophenyl)sulfanyl]-5-phenylcyclohexane-1,3-dione(Non-covalent)

36V.3: 13 residues within 4Å: Chain A: 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.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.237, A:I.241, A:I.241, A:T.247 Hydrogen bonds: A:N.137, A:R.168, A:R.168 Water bridges: A:D.165 pi-Stacking: A:Y.238 36V.9: 13 residues within 4Å: Chain C: 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.7 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.237, C:A.237, C:I.241, C:I.241, C:T.247 Hydrogen bonds: C:N.137, C:R.168, C:R.168 pi-Stacking: C:Y.238 36V.11: 13 residues within 4Å: Chain D: 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 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:A.237, D:I.241, D:I.241, D:T.247 Hydrogen bonds: D:N.137, D:R.168, D:R.168, D:T.247 pi-Stacking: D:Y.238

1 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.5: 9 residues within 4Å: Chain B: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.237 Hydrogen bonds: B:R.105, B:N.137, B:H.192, B:T.247, B:T.247 Salt bridges: B:R.105, B:R.168, B:H.192

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

SO4.12: 5 residues within 4Å: Chain B: L.182, H.185 Chain D: R.170, L.182, H.185 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:L.182 Water bridges: D:R.170, B:H.185, B:H.185, B:A.206 Salt bridges: D:R.170, D:H.185, B:H.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dragovich, P.S. et al., Identification of substituted 3-hydroxy-2-mercaptocyclohex-2-enones as potent inhibitors of human lactate dehydrogenase. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-07-16

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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