SMTL ID : 6bb1.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 22 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, I.115, F.118, I.119, V.135, S.136, N.137, L.164, H.192, T.247, I.251 Ligands: D3J.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.30, A:L.164, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:V.52, A:V.135, A:N.137, A:N.137 Water bridges: A:G.28, A:G.31 NAD.3: 21 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, I.115, I.119, V.135, S.136, N.137, S.160, L.164, H.192, T.247, I.251 Ligands: D3J.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:N.137, B:N.137, B:S.160, B:H.192 NAD.6: 22 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, S.160, L.164, H.192, T.247, I.251 Ligands: D3J.8 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:I.251 Hydrogen bonds: C:V.27, C:A.29, C:V.30, C:V.52, C:G.96, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:G.31, C:S.160, C:L.164 NAD.9: 24 residues within 4Å: Chain D: V.25, G.28, A.29, V.30, D.51, V.52, I.53, 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 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:V.30, D:I.251, D:I.251 Hydrogen bonds: D:A.29, D:V.30, D:V.52, D:G.96, D:A.97, D:N.112, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31, D:Y.82, D:R.98, D:R.105, D:R.168 Salt bridges: D:R.98, D:R.98

3 x D3J: (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one(Non-covalent)

D3J.2: 13 residues within 4Å: Chain A: N.137, P.138, L.164, D.165, R.168, H.192, G.193, D.194, A.237, Y.238, I.241, T.247 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.237, A:A.237, A:I.241 Hydrogen bonds: A:N.137, A:R.168, A:R.168, A:H.192 pi-Stacking: A:Y.238 D3J.5: 16 residues within 4Å: Chain B: N.137, P.138, L.164, D.165, R.168, H.192, G.193, D.194, V.233, V.234, A.237, Y.238, I.241, Y.246, T.247 Ligands: NAD.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.137, B:A.237, B:I.241 Hydrogen bonds: B:N.137, B:R.168, B:R.168, B:H.192, B:T.247 pi-Stacking: B:Y.238 D3J.8: 15 residues within 4Å: Chain C: R.105, N.137, P.138, L.164, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, T.247 Ligands: NAD.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:N.137, C:A.237, C:I.241 Hydrogen bonds: C:N.137, C:R.168, C:R.168, C:H.192, C:T.247 pi-Stacking: C:Y.238

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

SO4.4: 3 residues within 4Å: Chain B: W.147, P.153, K.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.154 SO4.7: 4 residues within 4Å: Chain C: W.147, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.154 SO4.10: 3 residues within 4Å: Chain D: W.147, P.153, K.154 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.154 Salt bridges: D:K.154

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
E

B
F

C
G

D
H

L-lactate dehydrogenase A chain

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