SMTL ID : 6mva.1

LDHA structure in complex with inhibitor 14

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 22 residues within 4Å: Chain A: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 Ligands: D4S.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.165, A:I.252, A:I.252, A:I.252 Hydrogen bonds: A:V.28, A:V.31, A:V.53, A:Y.83, A:G.97, A:V.136, A:N.138, A:N.138 Water bridges: A:G.29, A:G.32 NAI.5: 23 residues within 4Å: Chain B: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: D4S.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252, B:I.252, 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, B:S.161 Water bridges: B:G.29, B:G.32 NAI.8: 22 residues within 4Å: Chain C: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 Ligands: D4S.10 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:L.165, C:I.252, C:I.252 Hydrogen bonds: C:V.28, C:G.29, C:V.31, C:V.53, C:G.97, C:V.136, C:N.138, C:N.138 Water bridges: C:A.30, C:A.30, C:G.32 NAI.11: 22 residues within 4Å: Chain D: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, V.140, L.165, H.193, T.248, I.252 Ligands: D4S.13 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138 Water bridges: D:G.29, D:G.29, D:A.30, D:A.30

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: W.148, G.152, F.153, P.154, K.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.155 Water bridges: A:N.156 EPE.6: 5 residues within 4Å: Chain B: W.148, G.152, F.153, P.154, K.155 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.155 EPE.9: 5 residues within 4Å: Chain C: W.148, G.152, F.153, P.154, K.155 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.155

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

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 C, 4 interactions with chain A Water bridges: C:L.183, C:A.207, A:R.171, A:H.186 Salt bridges: C:H.186, A:R.171, A:H.186 SO4.12: 6 residues within 4Å: Chain B: L.183, S.184, H.186 Chain D: R.171, H.186, W.188 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Water bridges: B:A.207, D:R.171, D:V.270 Salt bridges: B:H.186, D:R.171, D:H.186

4 x D4S: (6R)-6-(3-aminophenyl)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one(Non-covalent)

D4S.4: 15 residues within 4Å: Chain A: V.31, N.138, L.165, D.166, R.169, H.193, G.194, D.195, V.235, A.238, Y.239, I.242, Y.247, T.248 Ligands: NAI.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.238, A:I.242, A:I.242 Hydrogen bonds: A:N.138, A:H.193, A:T.248, A:T.248 Salt bridges: A:R.169 pi-Stacking: A:Y.239 D4S.7: 15 residues within 4Å: Chain B: V.31, N.138, L.165, D.166, R.169, H.193, G.194, V.234, V.235, A.238, Y.239, I.242, Y.247, T.248 Ligands: NAI.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.238, B:I.242 Hydrogen bonds: B:N.138, B:H.193, B:T.248, B:T.248, B:T.248 Salt bridges: B:R.169 pi-Stacking: B:Y.239 D4S.10: 15 residues within 4Å: Chain C: V.31, N.138, D.166, R.169, H.193, G.194, D.195, V.234, V.235, A.238, Y.239, I.242, Y.247, T.248 Ligands: NAI.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.235, C:A.238, C:I.242, C:I.242 Hydrogen bonds: C:N.138, C:H.193, C:T.248, C:T.248 Salt bridges: C:R.169 pi-Stacking: C:Y.239 D4S.13: 16 residues within 4Å: Chain D: V.31, N.138, L.165, D.166, R.169, H.193, G.194, D.195, V.234, V.235, A.238, Y.239, I.242, Y.247, T.248 Ligands: NAI.11 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.235, D:A.238, D:I.242, D:I.242 Hydrogen bonds: D:N.138, D:H.193, D:T.248, D:T.248, D:T.248 Salt bridges: D:R.169 pi-Stacking: D:Y.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wei, B. et al., Structure-based Optimization of Potent, Cell-ActiveHydroxylactam Inhibitors of Lactate Dehydrogenase. To Be Published

Release Date

2019-10-30

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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