SMTL ID : 4qo8.1

Lactate Dehydrogenase A in complex with substituted 3-Hydroxy-2-mercaptocyclohex-2-enone compound 104

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: 36U.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.251 Hydrogen bonds: A:G.28, A:A.29, A:V.30, A:V.52, A:G.96, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.31 Salt bridges: A:R.98, A:R.98 NAI.5: 27 residues within 4Å: Chain B: V.25, G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, Q.99, 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: LAC.7 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, B:G.96, 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 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.9: 23 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, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: 36U.12 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:T.247 Hydrogen bonds: C:V.27, 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.28, C:G.31, C:Y.82 NAI.13: 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, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: 36U.15 11 PLIP interactions: 11 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:G.31, D:Y.82

3 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.154 Salt bridges: A:K.154 EPE.6: 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.10: 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 SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: R.170, H.185 Chain C: L.182, H.185 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Water bridges: C:L.182, C:A.206, A:R.170, A:R.170, A:H.185 Salt bridges: C:H.185, A:R.170, A:H.185 SO4.8: 4 residues within 4Å: Chain B: R.170, H.185 Chain D: S.183, H.185 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Water bridges: B:H.185, B:H.185, B:V.269 Salt bridges: B:R.170, B:H.185, D:H.185 SO4.11: 5 residues within 4Å: Chain A: L.182, S.183, H.185 Chain C: R.170, H.185 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:L.182 Salt bridges: A:H.185, C:R.170, C:H.185 Water bridges: C:R.170, C:R.170, C:R.170, C:W.187 SO4.14: 5 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain B Water bridges: D:R.170, D:W.187, B:L.182, B:H.185 Salt bridges: D:R.170, D:H.185, B:H.185

3 x 36U: (5S)-2-[(2-chlorophenyl)sulfanyl]-5-(2,6-dichlorophenyl)-3-hydroxycyclohex-2-en-1-one(Non-covalent)

36U.4: 13 residues within 4Å: Chain A: 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.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: 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 36U.12: 12 residues within 4Å: Chain C: N.137, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, T.247 Ligands: NAI.9 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.234, C:A.237, C:I.241, C:T.247 Hydrogen bonds: C:N.137, C:R.168, C:R.168, C:H.192 36U.15: 12 residues within 4Å: Chain D: N.137, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, T.247 Ligands: NAI.13 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: 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:T.247

1 x LAC: LACTIC ACID(Non-covalent)

LAC.7: 10 residues within 4Å: Chain B: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, I.241, T.247 Ligands: NAI.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.237 Hydrogen bonds: B:R.105, B:N.137, B:T.247, B:T.247 Salt bridges: B:R.105, B:R.168, B:H.192

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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