SMTL ID : 5ixy.1

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 31: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 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, Y.82, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, L.164, H.192, I.251 Ligands: GN2.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251, A:I.251, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:G.31, A:V.52, A:K.56, A:K.56, A:Y.82, A:G.96, A:V.135, A:N.137, A:N.137, A:S.160 Salt bridges: A:R.98 NAD.5: 23 residues within 4Å: Chain B: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, L.164, H.192, I.251 Ligands: GN2.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.164, B:I.251, B:I.251, B:I.251 Hydrogen bonds: B:V.27, B:A.29, B:V.30, B:G.31, B:V.52, B:Y.82, B:G.96, B:V.135, B:N.137, B:N.137, B:S.160 Salt bridges: B:R.98 NAD.10: 24 residues within 4Å: Chain C: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, S.160, L.164, H.192, I.251 Ligands: GN2.13 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:L.164, C:I.251, C:I.251, C:I.251 Hydrogen bonds: C:V.27, C:A.29, C:V.30, C:G.31, C:V.52, C:Y.82, C:G.96, C:V.135, C:N.137, C:N.137, C:S.160 Salt bridges: C:R.98 NAD.14: 24 residues within 4Å: Chain D: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, I.115, F.118, I.119, V.135, S.136, N.137, S.160, L.164, H.192, I.251 Ligands: GN2.15 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:L.164, D:I.251, D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:G.31, D:V.52, D:Y.82, D:G.96, D:V.135, D:N.137, D:N.137, D:S.160

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

SO4.2: 5 residues within 4Å: Chain A: L.182, S.183, H.185 Chain C: R.170, H.185 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.183 Salt bridges: A:H.185, C:R.170, 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, W.187 Chain D: L.182, 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: 6 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185, W.187 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:R.170, D:H.185, B:H.185 SO4.8: 3 residues within 4Å: Chain B: W.147, P.153, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.154 Salt bridges: B:K.154 SO4.11: 6 residues within 4Å: Chain A: R.170, H.185, W.187 Chain C: L.182, S.183, H.185 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Salt bridges: A:R.170, A:H.185, C:H.185 SO4.12: 3 residues within 4Å: Chain C: W.147, P.153, K.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.154

4 x GN2: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one(Non-covalent)

GN2.4: 14 residues within 4Å: Chain A: R.98, N.137, L.164, D.165, R.168, H.192, G.193, V.234, A.237, Y.238, I.241, G.245, T.247 Ligands: NAD.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.234, A:A.237, A:I.241, A:I.241 Hydrogen bonds: A:R.98, A:N.137, A:R.168, A:R.168 pi-Stacking: A:Y.238 GN2.9: 14 residues within 4Å: Chain B: R.98, N.137, L.164, D.165, R.168, H.192, G.193, D.194, A.237, Y.238, I.241, G.245, T.247 Ligands: NAD.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.237, B:I.241, B:I.241 Hydrogen bonds: B:R.98, B:N.137, B:R.168, B:R.168, B:T.247 pi-Stacking: B:Y.238 GN2.13: 15 residues within 4Å: Chain C: R.98, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, G.245, T.247 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.234, C:A.237, C:I.241, C:I.241 Hydrogen bonds: C:N.137, C:R.168, C:R.168 pi-Stacking: C:Y.238 GN2.15: 15 residues within 4Å: Chain D: Q.99, N.137, L.164, D.165, R.168, H.192, G.193, D.194, V.234, A.237, Y.238, I.241, G.245, T.247 Ligands: NAD.14 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.234, D:A.237, D:I.241, D:I.241 Hydrogen bonds: D:N.137, D:R.168, D:R.168, D:T.247 pi-Stacking: D:Y.238

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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