SMTL ID : 5w8j.1

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-tetramer

Ligands

6 x 9Y7: 2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid(Non-covalent)

9Y7.1: 18 residues within 4Å: Chain A: Q.100, L.109, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, D.195, A.238, I.242, T.248, L.323 Ligands: DMS.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.100 Hydrogen bonds: A:N.138, A:D.141, A:D.141, A:I.142, A:E.192 Water bridges: A:H.193, A:D.195 Salt bridges: A:R.169, A:H.193 9Y7.2: 13 residues within 4Å: Chain A: V.26, G.27, V.51, D.52, V.53, K.81, Y.83, A.96, G.97, A.98, I.116, F.119, I.120 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.53, A:A.96, A:I.116, A:F.119, A:I.120 Hydrogen bonds: A:K.81 Water bridges: A:G.97 pi-Stacking: A:F.119 9Y7.8: 13 residues within 4Å: Chain B: V.26, G.27, V.51, D.52, V.53, K.81, Y.83, A.96, G.97, R.99, I.116, F.119, I.120 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.53, B:V.53, B:A.96, B:I.116, B:F.119, B:I.120 Hydrogen bonds: B:K.81 Water bridges: B:G.97, B:G.97, B:R.99, B:R.99 Salt bridges: B:R.99 pi-Stacking: B:F.119 Halogen bonds: B:V.51 9Y7.11: 16 residues within 4Å: Chain C: Q.100, R.106, L.109, N.138, P.139, V.140, D.141, I.142, R.169, E.192, H.193, G.194, T.248, I.252, L.323 Ligands: DMS.13 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:N.138, C:P.139 Hydrogen bonds: C:N.138, C:D.141, C:I.142, C:E.192 Water bridges: C:R.169, C:H.193, C:D.195 Salt bridges: C:R.169, C:H.193 9Y7.12: 13 residues within 4Å: Chain C: V.26, G.27, V.51, D.52, V.53, K.81, Y.83, A.96, G.97, A.98, I.116, F.119, I.120 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.53, C:V.53, C:A.96, C:I.116, C:I.116, C:F.119, C:I.120 Water bridges: C:G.97, C:R.99, C:R.99, C:R.99 pi-Stacking: C:F.119 9Y7.15: 19 residues within 4Å: Chain D: Q.100, R.106, L.109, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, A.238, I.242, T.248, L.323 Ligands: DMS.16, DMS.17 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:N.138 Hydrogen bonds: D:N.138, D:D.141, D:I.142, D:E.192, D:E.192, D:T.248, D:T.248 Water bridges: D:D.195 Salt bridges: D:R.169, D:H.193

5 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 7 residues within 4Å: Chain A: R.171, H.186, W.188, V.270 Chain C: L.183, S.184, H.186 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Water bridges: C:A.207, A:R.171, A:R.171, A:W.188, A:W.188 Salt bridges: C:H.186, C:H.186, A:R.171, A:H.186 MLA.7: 8 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.138, B:T.248, B:T.248 Water bridges: B:T.248 Salt bridges: B:R.106, B:R.106, B:R.169, B:H.193, B:H.193 MLA.9: 6 residues within 4Å: Chain B: R.171, H.186, W.188, V.270 Chain D: S.184, H.186 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:V.270 Water bridges: B:R.171, B:R.171, B:H.186, B:W.188, D:H.186 Salt bridges: B:R.171, B:H.186, D:H.186, D:H.186 MLA.10: 6 residues within 4Å: Chain A: S.184, H.186 Chain C: R.171, H.186, W.188, V.270 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain A Water bridges: C:R.171, C:R.171, C:H.186, C:W.188, A:H.186 Salt bridges: C:R.171, C:H.186, A:H.186, A:H.186 MLA.14: 6 residues within 4Å: Chain B: S.184, H.186 Chain D: R.171, H.186, W.188, V.270 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Water bridges: B:A.207, D:R.171, D:R.171, D:V.270 Salt bridges: B:H.186, B:H.186, D:R.171, D:H.186

5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: Y.239, I.242 Ligands: 9Y7.1 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.239 DMS.5: 3 residues within 4Å: Chain A: T.213, L.214 Chain C: T.307 No protein-ligand interaction detected (PLIP) DMS.13: 3 residues within 4Å: Chain C: Y.239, I.242 Ligands: 9Y7.11 No protein-ligand interaction detected (PLIP) DMS.16: 5 residues within 4Å: Chain D: G.97, A.98, S.137, N.138 Ligands: 9Y7.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.138 Water bridges: D:N.138, D:N.138 DMS.17: 3 residues within 4Å: Chain D: Y.239, I.242 Ligands: 9Y7.15 1 PLIP interactions: 1 interactions with chain D pi-Cation interactions: D:Y.239

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 12 residues within 4Å: Chain A: S.202, G.203, M.204, N.205, G.208, S.210 Chain C: S.202, G.203, M.204, N.205, G.208, S.210 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:S.202, C:M.204, C:N.205, A:G.203, A:N.205 Water bridges: C:S.210, C:L.211, A:S.210, A:L.211 GOL.18: 10 residues within 4Å: Chain B: G.203, N.205, G.208, S.210 Chain D: S.202, G.203, M.204, N.205, G.208, S.210 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:G.203, D:N.205, B:G.203, B:N.205 Water bridges: D:L.211, B:S.202

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
B

C
C

D
D

L-lactate dehydrogenase A chain

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