SMTL ID : 6bad.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: 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, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0Y.5 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:V.52, A:G.96, A:R.98, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.28, A:G.31, A:K.56, A:Y.82, A:A.95, A:G.96, A:R.98 Salt bridges: A:R.98, A:R.98 NAD.6: 27 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, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0Y.10 20 PLIP interactions: 20 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:G.96, B:R.98, B:V.135, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31 Salt bridges: B:K.56, B:R.98, B:R.98 NAD.11: 27 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, 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: D0Y.17 23 PLIP interactions: 23 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:R.98, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:G.31, C:A.95, C:G.96 Salt bridges: C:K.56, C:R.98, C:R.98 NAD.18: 28 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, L.108, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: D0Y.20 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:L.164, 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:R.98, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31, D:A.95, D:R.98, D:R.98, D:N.112 Salt bridges: D:K.56, D:R.98, D:R.98

7 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 Water bridges: A:N.155 EPE.3: 7 residues within 4Å: Chain A: Q.99, R.105, L.108, N.137, P.138, Y.238 Ligands: D0Y.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.99, A:Y.238 Water bridges: A:R.105, A:N.137, A:N.137, A:N.137 Salt bridges: A:R.105, A:D.194, A:D.194 EPE.7: 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: 7 residues within 4Å: Chain B: Q.99, R.105, L.108, N.137, P.138, Y.238 Ligands: D0Y.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.99 Water bridges: B:Q.99, B:R.105, B:N.137 Salt bridges: B:R.105, B:D.194 EPE.12: 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 EPE.13: 7 residues within 4Å: Chain C: Q.99, R.105, L.108, N.137, P.138, Y.238 Ligands: D0Y.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Q.99 Water bridges: C:R.105, C:N.137 Salt bridges: C:R.105, C:D.194, C:D.194 EPE.16: 3 residues within 4Å: Chain C: D.194, E.235, Y.238 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:D.194, C:E.235, C:E.235

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

SO4.4: 4 residues within 4Å: Chain A: R.170, H.185 Chain C: L.182, H.185 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Water bridges: A:R.170, A:H.185, C:L.182, C:A.206 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.9: 4 residues within 4Å: Chain B: R.170, H.185 Chain D: L.182, H.185 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Water bridges: D:A.206 Salt bridges: D:H.185, B:R.170, B:H.185 SO4.14: 3 residues within 4Å: Chain C: H.214, P.215, D.216 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.214, C:D.216 Salt bridges: C:H.214 SO4.15: 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:R.170, A:A.206 Salt bridges: C:R.170, C:H.185, A:H.185 Hydrogen bonds: A:L.182 SO4.19: 4 residues within 4Å: Chain B: L.182, H.185 Chain D: R.170, H.185 9 PLIP interactions: 6 interactions with chain D, 3 interactions with chain B Water bridges: D:R.170, D:R.170, D:R.170, D:V.269, B:L.182, B:A.206 Salt bridges: D:R.170, D:H.185, B:H.185

4 x D0Y: (6R)-3-[(2-chlorophenyl)sulfanyl]-6-{3-[(4-fluorophenyl)amino]phenyl}-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one(Non-covalent)

D0Y.5: 17 residues within 4Å: Chain A: R.98, Q.99, Q.100, 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: NAD.1, EPE.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.98, A:Q.99, A:V.234, A:A.237, A:Y.238, A:I.241, A:I.241 Hydrogen bonds: A:Q.99, A:N.137, A:H.192 Salt bridges: A:R.168 pi-Stacking: A:Y.238 D0Y.10: 18 residues within 4Å: Chain B: R.98, Q.99, Q.100, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, Y.246, T.247 Ligands: NAD.6, EPE.8 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:R.98, B:Q.99, B:V.234, B:A.237, B:Y.238, B:I.241, B:I.241 Hydrogen bonds: B:Q.99, B:N.137, B:H.192, B:T.247 Salt bridges: B:R.168 pi-Stacking: B:Y.238 D0Y.17: 17 residues within 4Å: Chain C: R.98, Q.99, Q.100, 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: NAD.11, EPE.13 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:R.98, C:Q.99, C:V.234, C:A.237, C:Y.238, C:I.241 Hydrogen bonds: C:Q.99, C:N.137, C:H.192 Salt bridges: C:R.168 pi-Stacking: C:Y.238 D0Y.20: 17 residues within 4Å: Chain D: R.98, Q.99, Q.100, R.105, 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: NAD.18 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:R.98, 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:H.192 Salt bridges: D:R.168 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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