SMTL ID : 6bb3.1

Lactate Dehydrogenase in complex with inhibitor 3-((2-chlorophenyl)thio)-6-(6-((4-fluorophenyl)amino)pyridin-2-yl)-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 23 residues within 4Å: Chain A: V.25, G.26, V.27, 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, L.164, H.192, T.247, I.251 Ligands: D4A.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.164, A:T.247, A:I.251, A:I.251 Hydrogen bonds: A:V.27, 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.28, A:G.31 Salt bridges: A:R.98 NAD.5: 25 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, T.94, A.95, G.96, A.97, R.98, I.115, I.119, V.135, S.136, N.137, L.164, H.192, T.247, I.251 Ligands: D4A.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.164, B:T.247, B:I.251, B:I.251 Hydrogen bonds: B:V.27, B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, B:G.96, B:G.96, B:R.98, B:V.135, B:N.137, B:N.137 Water bridges: B:G.28, B:G.31 Salt bridges: B:K.56, B:R.98, B:R.98 NAD.9: 23 residues within 4Å: Chain C: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, I.115, I.119, V.135, S.136, N.137, L.164, H.192, T.247, I.251 Ligands: D4A.12 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:V.27, C:A.29, C:V.30, C:V.52, C:K.56, C:K.56, C:G.96, C:V.135, C:N.137, C:N.137 Salt bridges: C:K.56 NAD.13: 25 residues within 4Å: Chain D: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, I.115, I.119, V.135, S.136, N.137, L.164, H.192, T.247, I.251 Ligands: D4A.15 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:T.247, D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:V.52, D:K.56, D:K.56, D:G.96, D:A.97, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31 Salt bridges: D:K.56, D:R.98, D:R.98

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

SO4.2: 4 residues within 4Å: Chain A: R.170, H.185 Chain C: L.182, H.185 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Water bridges: A:H.185, A:W.187 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.3: 3 residues within 4Å: Chain A: W.147, P.153, K.154 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.154 SO4.6: 5 residues within 4Å: Chain B: R.170, H.185 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 SO4.7: 4 residues within 4Å: Chain B: W.147, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.154 SO4.10: 3 residues within 4Å: Chain A: H.185 Chain C: R.170, H.185 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Water bridges: C:H.185, C:W.187 Salt bridges: C:R.170, C:H.185, A:H.185 Hydrogen bonds: A:L.182 SO4.11: 4 residues within 4Å: Chain C: W.147, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.154 Water bridges: C:F.152 SO4.14: 4 residues within 4Å: Chain B: L.182, H.185 Chain D: R.170, H.185 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Water bridges: B:A.206, D:R.170, D:R.170 Salt bridges: B:H.185, D:R.170, D:H.185

4 x D4A: (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{6-[(4-fluorophenyl)amino]pyridin-2-yl}-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one(Non-covalent)

D4A.4: 16 residues within 4Å: Chain A: Q.99, R.105, L.108, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.108, A:N.137, A:A.237, A:I.241, A:I.241, A:T.247 Hydrogen bonds: A:N.137, A:H.192 Salt bridges: A:R.168 pi-Stacking: A:Y.238 D4A.8: 15 residues within 4Å: Chain B: R.98, N.137, P.138, L.164, D.165, R.168, H.192, G.193, D.194, A.237, Y.238, I.241, Y.246, T.247 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.237, B:I.241, B:I.241, B:T.247 Hydrogen bonds: B:N.137, B:H.192 Salt bridges: B:R.168 pi-Stacking: B:Y.238 D4A.12: 13 residues within 4Å: Chain C: 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.9 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:N.137, C:A.237, C:I.241 Hydrogen bonds: C:N.137, C:H.192 Salt bridges: C:R.168 pi-Stacking: C:Y.238 D4A.15: 14 residues within 4Å: Chain D: R.98, 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.13 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:A.237, D:I.241, D:I.241, D:T.247 Hydrogen bonds: D:N.137, D:H.192 Salt bridges: D:R.168 pi-Stacking: D:Y.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, B.Q. 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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