SMTL ID : 5ixs.1

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 9: (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.154 Water bridges: A:N.155 EPE.5: 5 residues within 4Å: Chain B: W.147, G.151, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.154 Salt bridges: B:K.154 EPE.9: 4 residues within 4Å: Chain C: W.147, G.151, P.153, K.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.154

3 x TXD: 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

TXD.2: 24 residues within 4Å: Chain A: V.25, 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, S.160, L.164, H.192, T.247, I.251 Ligands: 6EY.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.164, A:T.247, 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:T.247 Salt bridges: A:R.98, A:R.98 TXD.6: 24 residues within 4Å: Chain B: V.25, G.26, 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: 6EY.7 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:V.30, 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:A.97, B:V.135, B:N.137, B:N.137 Water bridges: B:G.28, B:G.31, B:R.98, B:R.98 Salt bridges: B:K.56, B:R.98, B:R.98 TXD.13: 24 residues within 4Å: Chain D: V.25, 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, S.160, L.164, H.192, T.247, I.251 Ligands: 6EY.14 19 PLIP interactions: 19 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:A.97, D:R.98, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.31, D:T.247 Salt bridges: D:R.98, D:R.98

4 x 6EY: (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one(Non-covalent)

6EY.3: 15 residues within 4Å: Chain A: R.98, 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: TXD.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.98, A:V.234, A:A.237, A:I.241, A:I.241, A:T.247 Hydrogen bonds: A:R.98, A:N.137, A:R.168, A:R.168, A:H.192, A:T.247 pi-Stacking: A:Y.238 6EY.7: 15 residues within 4Å: Chain B: R.98, N.137, L.164, D.165, R.168, H.192, G.193, V.233, V.234, A.237, Y.238, I.241, Y.246, T.247 Ligands: TXD.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:R.98, 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, B:T.247 pi-Stacking: B:Y.238 6EY.11: 15 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, Y.246, T.247 Ligands: NAI.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:R.98, C:V.234, C:A.237, C:I.241, C:T.247 Hydrogen bonds: C:R.98, C:N.137, C:R.168, C:R.168, C:H.192, C:T.247 pi-Stacking: C:Y.238 6EY.14: 16 residues within 4Å: Chain D: R.98, Q.99, N.137, 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: TXD.13 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:R.98, D:Q.99, D:A.237, D:I.241, D:I.241 Hydrogen bonds: D:R.98, D:N.137, D:R.168, D:R.168, D:H.192, D:T.247, D:T.247 pi-Stacking: D:Y.238

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

SO4.4: 5 residues within 4Å: Chain A: R.170, H.185 Chain C: S.183, H.185 Ligands: SO4.12 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Water bridges: A:R.170, A:R.170, A:W.187, C:L.182, C:A.206 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.8: 6 residues within 4Å: Chain B: R.170, H.185 Chain D: L.182, S.183, H.185 Ligands: SO4.15 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Water bridges: D:S.183, D:A.206, B:R.170, B:R.170 Salt bridges: D:H.185, B:R.170, B:H.185 SO4.12: 4 residues within 4Å: Chain A: H.185 Chain C: R.170, H.185 Ligands: SO4.4 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Water bridges: C:R.170, C:H.185, A:A.206 Salt bridges: C:R.170, C:H.185, A:H.185 Hydrogen bonds: A:L.182 SO4.15: 4 residues within 4Å: Chain B: H.185 Chain D: R.170, H.185 Ligands: SO4.8 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain D Water bridges: B:A.206, D:R.170, D:R.170, D:V.269 Salt bridges: B:H.185, D:R.170, D:H.185

1 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.10: 22 residues within 4Å: Chain C: 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, L.164, H.192, T.247, I.251 Ligands: 6EY.11 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.30, C:T.247, C:I.251, C:I.251 Hydrogen bonds: C:V.27, 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 Water bridges: C:G.28, C:G.31 Salt bridges: C:R.98, C:R.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Purkey, H.E. et al., Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice. Acs Med.Chem.Lett. (2016)

Release Date

2016-09-14

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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