SMTL ID : 4zvv.1

Lactate dehydrogenase A in complex with a trisubstituted piperidine-2,4-dione inhibitor GNE-140

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 20 residues within 4Å: Chain A: G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, I.120, V.136, S.137, N.138, L.165, H.193, T.248, I.252 Ligands: GN0.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.165, A:T.248, A:I.252 Hydrogen bonds: A:G.29, A:V.31, A:V.53, A:G.97, A:V.136, A:N.138, A:N.138 Water bridges: A:G.32, A:Y.83, A:G.97, A:R.99, A:R.99, A:H.193, A:H.193 Salt bridges: A:R.99 NAD.6: 19 residues within 4Å: Chain B: G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, I.120, V.136, N.138, L.165, H.193, I.252 Ligands: GN0.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252 Hydrogen bonds: B:V.28, B:A.30, B:V.31, B:V.53, B:G.97, B:V.136, B:N.138, B:N.138 Water bridges: B:G.32 Salt bridges: B:R.99 NAD.10: 21 residues within 4Å: Chain C: V.26, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, I.120, V.136, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: GN0.12 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:V.136, C:I.252 Hydrogen bonds: C:A.30, C:V.31, C:V.53, C:G.97, C:V.136, C:N.138, C:N.138, C:S.161 Water bridges: C:G.29, C:G.32, C:G.97, C:A.98, C:R.99, C:R.99, C:R.99 Salt bridges: C:R.99 NAD.13: 24 residues within 4Å: Chain D: V.26, G.27, V.28, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, F.119, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: GN0.15 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252 Hydrogen bonds: D:V.28, D:G.29, D:A.30, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.32

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

SO4.2: 5 residues within 4Å: Chain A: L.183, S.184, H.186 Chain C: R.171, H.186 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:S.184 Water bridges: A:A.207 Salt bridges: A:H.186, C:R.171, C:H.186 SO4.3: 5 residues within 4Å: Chain A: R.171, H.186 Chain C: L.183, S.184, H.186 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Water bridges: A:W.188, C:L.183, C:H.186, C:H.186 Salt bridges: A:R.171, A:H.186, C:H.186 SO4.4: 3 residues within 4Å: Chain A: W.148, P.154, K.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.155 Salt bridges: A:K.155 SO4.7: 4 residues within 4Å: Chain B: R.171, H.186 Chain D: L.183, H.186 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:L.183 Salt bridges: D:H.186, B:R.171, B:H.186 Water bridges: B:H.186, B:W.188 SO4.8: 4 residues within 4Å: Chain B: W.148, F.153, P.154, K.155 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.155 Salt bridges: B:K.155 SO4.11: 3 residues within 4Å: Chain C: W.148, P.154, K.155 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.155 Water bridges: C:F.153 SO4.14: 5 residues within 4Å: Chain B: L.183, H.186 Chain D: R.171, H.186, W.188 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Salt bridges: D:R.171, D:H.186, B:H.186 Hydrogen bonds: B:L.183

4 x GN0: (2~{R})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one(Non-covalent)

GN0.5: 16 residues within 4Å: Chain A: R.99, N.138, L.165, D.166, R.169, H.193, G.194, D.195, V.235, A.238, Y.239, I.242, G.246, Y.247, T.248 Ligands: NAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.235, A:A.238, A:I.242, A:I.242, A:T.248 Hydrogen bonds: A:N.138, A:R.169, A:R.169, A:H.193 pi-Stacking: A:Y.239 GN0.9: 14 residues within 4Å: Chain B: R.99, N.138, L.165, D.166, R.169, H.193, G.194, D.195, A.238, Y.239, I.242, G.246, T.248 Ligands: NAD.6 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.238, B:I.242, B:I.242 Hydrogen bonds: B:R.99, B:N.138, B:R.169, B:R.169, B:H.193, B:T.248, B:T.248 pi-Stacking: B:Y.239 GN0.12: 14 residues within 4Å: Chain C: R.99, N.138, L.165, D.166, R.169, H.193, G.194, D.195, A.238, Y.239, I.242, G.246, T.248 Ligands: NAD.10 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:A.238, C:I.242, C:I.242 Hydrogen bonds: C:N.138, C:R.169, C:R.169, C:H.193, C:T.248 pi-Stacking: C:Y.239 GN0.15: 14 residues within 4Å: Chain D: Q.100, N.138, L.165, D.166, R.169, H.193, G.194, D.195, A.238, Y.239, I.242, G.246, T.248 Ligands: NAD.13 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.238, D:I.242, D:I.242 Hydrogen bonds: D:N.138, D:R.169, D:R.169, D:H.193, D:T.248, D:T.248 pi-Stacking: D:Y.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boudreau, A. et al., Metabolic plasticity underpins innate and acquired resistance to LDHA inhibition. Nat.Chem.Biol. (2016)

Release Date

2016-05-18

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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