SMTL ID : 6bag.1

Lactate Dehydrogenase in complex with inhibitor (R)-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 2.40 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.9: 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: 23 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, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0V.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251, A:I.251 Hydrogen bonds: A:V.27, 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, A:Y.82 NAD.6: 26 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, 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: D0V.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.164, 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:V.135, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31 Salt bridges: B:R.98 NAD.10: 23 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, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0V.12 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.164, C:I.251, C:I.251 Hydrogen bonds: C:V.27, C:A.29, C:V.30, C:V.52, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:G.31 NAD.13: 24 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, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0V.15 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:V.52, D:G.96, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31

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

4 x D0V: (2R)-5-[(2-chlorophenyl)sulfanyl]-6'-[(4-fluorophenyl)amino]-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro[2,2'-bipyridin]-6(1H)-one(Non-covalent)

D0V.4: 15 residues within 4Å: Chain A: L.108, 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.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.137, A:V.234, A:A.237, A:I.241 Hydrogen bonds: A:N.137, A:R.168, A:R.168, A:H.192, A:T.247 pi-Stacking: A:Y.238 D0V.8: 15 residues within 4Å: Chain B: L.108, 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 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:N.137, B:V.234, B:A.237, B:I.241, 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 D0V.12: 15 residues within 4Å: Chain C: 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, T.247 Ligands: NAD.10 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:N.137, C:V.234, C:A.237, C:I.241, C:I.241 Hydrogen bonds: C:N.137, C:R.168, C:R.168, C:H.192 pi-Stacking: C:Y.238 D0V.15: 16 residues within 4Å: Chain D: Q.99, L.108, 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.13 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:N.137, D:V.234, D:A.237, D:I.241, D:I.241 Hydrogen bonds: D:N.137, D:R.168, D:R.168, D:H.192, D:T.247 Water bridges: D:Y.238 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

2018-10-17

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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