SMTL ID : 5w8l.1 (1 other biounit)

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and NADH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 26 residues within 4Å: Chain A: V.26, G.27, V.28, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: 9YA.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:L.165, A:I.252, A:I.252, A:I.252 Hydrogen bonds: A:V.28, A:G.29, A:V.31, A:V.53, A:G.97, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:G.32, A:R.99, A:R.99, A:R.99, A:N.113, A:N.113, A:N.113 Salt bridges: A:R.99 NAI.7: 25 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, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: 9YA.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.31, B:L.165, B:I.252, B:I.252 Hydrogen bonds: B:V.28, B:G.29, B:V.31, B:V.53, B:G.97, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:A.30, B:G.32, B:Y.83, B:Y.83, B:R.99, B:R.99, B:N.113 Salt bridges: B:R.99 NAI.13: 26 residues within 4Å: Chain C: V.26, G.27, V.28, G.29, A.30, V.31, D.52, V.53, I.54, T.95, A.96, G.97, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: 9YA.14 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:L.165, C:I.252, 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, C:S.161 Water bridges: C:G.32, C:R.99, C:R.99, C:R.99, C:N.113, C:N.113, C:N.113 Salt bridges: C:R.99 NAI.19: 25 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, R.99, I.116, F.119, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: 9YA.20 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:V.31, D:L.165, D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:G.29, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:A.30, D:G.32, D:Y.83, D:Y.83, D:R.99, D:R.99, D:N.113 Salt bridges: D:R.99

4 x 9YA: 2-{3-([1,1'-biphenyl]-3-yl)-5-(cyclopropylmethyl)-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid(Non-covalent)

9YA.2: 25 residues within 4Å: Chain A: R.106, L.107, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, V.235, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.1, EDO.4, EDO.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.106, A:R.106, A:L.107, A:L.109, A:V.110, A:N.138, A:P.139, A:A.238, A:Y.239, A:I.326 Hydrogen bonds: A:N.138, A:D.141, A:D.141, A:I.142, A:E.192, A:T.248 Salt bridges: A:R.169, A:H.193 9YA.8: 22 residues within 4Å: Chain B: Q.100, R.106, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323 Ligands: NAI.7, EDO.9 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:R.106, B:R.106, B:L.109, B:V.110, B:N.138, B:P.139, B:P.139, B:A.238, B:Y.239 Hydrogen bonds: B:N.138, B:D.141, B:D.141, B:D.141, B:I.142, B:E.192 Salt bridges: B:R.169, B:H.193 pi-Cation interactions: B:R.106 9YA.14: 25 residues within 4Å: Chain C: R.106, L.107, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, V.235, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.13, EDO.16, EDO.17 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:R.106, C:R.106, C:L.107, C:L.109, C:V.110, C:N.138, C:P.139, C:A.238, C:Y.239, C:I.326 Hydrogen bonds: C:N.138, C:D.141, C:D.141, C:I.142, C:E.192, C:T.248 Salt bridges: C:R.169, C:H.193 9YA.20: 22 residues within 4Å: Chain D: Q.100, R.106, L.109, V.110, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, Y.239, I.242, T.248, L.323 Ligands: NAI.19, EDO.21 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:R.106, D:R.106, D:L.109, D:V.110, D:N.138, D:P.139, D:P.139, D:A.238, D:Y.239 Hydrogen bonds: D:N.138, D:D.141, D:D.141, D:D.141, D:I.142, D:E.192 Salt bridges: D:R.169, D:H.193 pi-Cation interactions: D:R.106

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: L.12, L.13, K.14 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: R.106, Y.239, I.242 Ligands: 9YA.2 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: E.192, T.322, L.323 Ligands: 9YA.2 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: Y.281, K.305, V.306 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: R.106, Y.239, I.242 Ligands: 9YA.8, EDO.10 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: Y.239, I.242 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: R.177, E.229, V.230, Q.233 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: L.70 Chain B: N.164, S.167, R.171, P.272 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain C: L.12, L.13, K.14 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: R.106, Y.239, I.242 Ligands: 9YA.14 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: E.192, T.322, L.323 Ligands: 9YA.14 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: Y.281, K.305, V.306 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain D: R.106, Y.239, I.242 Ligands: 9YA.20, EDO.22 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: Y.239, I.242 Ligands: EDO.21 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain D: R.177, E.229, V.230, Q.233 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: L.70 Chain D: N.164, S.167, R.171, P.272 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rai, G. et al., Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH). J. Med. Chem. (2017)

Release Date

2018-01-17

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

L-lactate dehydrogenase A chain

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