SMTL ID : 6baz.1

Lactate Dehydrogenase in complex with inhibitor (S)-5-((2-chlorophenyl)thio)-6'-((4-fluorophenyl)amino)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro-[2,2'-bipyridin]-6(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 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.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

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.2: 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, S.160, L.164, H.192, T.247, I.251 Ligands: LAC.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.251 Hydrogen bonds: A:A.29, A:V.30, A:V.52, A:G.96, A:R.98, A:R.98, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.28 Salt bridges: A:R.98, A:R.98 NAD.6: 24 residues within 4Å: Chain B: G.26, 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 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.135, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:G.96, B:A.97, B:V.135, B:N.137, B:N.137, B:S.160 Salt bridges: B:R.98, B:R.98 NAD.9: 21 residues within 4Å: Chain C: G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, A.97, R.98, I.115, V.135, S.136, N.137, V.139, S.160, H.192, T.247, I.251 Ligands: D47.10 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:V.135, C:T.247, C:I.251, C:I.251, C:I.251 Hydrogen bonds: C:A.29, C:V.30, C:V.52, C:G.96, C:R.98, C:V.135, C:N.137, C:N.137, C:S.160 Salt bridges: C:R.98, C:R.98 NAD.11: 26 residues within 4Å: Chain D: V.25, G.26, V.27, 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, S.160, L.164, H.192, T.247, I.251 Ligands: D47.12 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:V.52, D:G.96, D:R.98, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31 Salt bridges: D:R.98, D:R.98

1 x LAC: LACTIC ACID(Non-covalent)

LAC.3: 8 residues within 4Å: Chain A: N.137, L.164, R.168, H.192, A.237, I.241, T.247 Ligands: NAD.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.241 Hydrogen bonds: A:N.137, A:H.192 Salt bridges: A:R.168, A:H.192

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

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

2 x D47: (3S,6S)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-6-(thiophen-3-yl)piperidine-2,4-dione(Non-covalent)

D47.10: 14 residues within 4Å: Chain C: R.98, N.137, L.164, D.165, R.168, H.192, G.193, V.233, V.234, A.237, Y.238, I.241, T.247 Ligands: NAD.9 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:R.98, C:R.98, C:V.234, C:A.237, C:Y.238, C:I.241, C:T.247 Hydrogen bonds: C:R.98, C:N.137, C:R.168, C:R.168 pi-Stacking: C:Y.238 D47.12: 18 residues within 4Å: Chain D: R.98, Q.99, Q.100, E.101, 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: NAD.11 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.98, D:Q.99, D:Q.99, D:V.234, D:A.237, D:Y.238, D:I.241, D:I.241 Hydrogen bonds: D:Q.99, D:N.137, D:R.168, D:R.168, D:T.247 pi-Stacking: D:Y.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, B. et al., Structure-guided optimization and in vivo activities of hydroxylactone and hydroxylactam Inhibitors of Human Lactate Dehydrogenase. To Be Published

Release Date

2018-10-24

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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