SMTL ID : 6q13.2 (1 other biounit)

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00420737-09 AT 2.00 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 23 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, I.116, F.119, I.120, V.136, S.137, N.138, L.165, H.193, T.248, I.252 Ligands: P8V.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:V.31, A:L.165, A:I.252, A:I.252, A:I.252 Hydrogen bonds: A:V.28, A:G.29, A:A.30, 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:Y.83, A:R.99, A:R.99, A:R.99, A:N.113 NAI.8: 23 residues within 4Å: Chain B: 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, L.165, H.193, T.248, I.252 Ligands: P8V.9 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.31, B:L.165, B:I.252, B:I.252, B:I.252 Hydrogen bonds: B:V.28, B:G.29, 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, B:Y.83, B:Y.83, B:R.99, B:R.99, B:R.99, B:N.113 NAI.15: 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: P8V.16 17 PLIP interactions: 17 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:A.30, C:G.32, C:R.99 Salt bridges: C:R.99 NAI.18: 26 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, 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: P8V.19 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252, 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:R.99 Salt bridges: D:R.99

4 x P8V: 2-[5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-3-{3-[(5-methylthiophen-2-yl)ethynyl]phenyl}-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid(Non-covalent)

P8V.2: 21 residues within 4Å: Chain A: 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.1, EDO.4 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:R.106, A:L.109, A:V.110, A:N.138, A:P.139, A:P.139, A:I.142, A:A.238, A:Y.239 Hydrogen bonds: A:N.138, A:D.141, A:D.141, A:D.141, A:I.142, A:T.248 Salt bridges: A:R.169, A:H.193 P8V.9: 21 residues within 4Å: Chain B: 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.8, EDO.11 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.106, B:L.109, B:V.110, B:N.138, B:P.139, B:P.139, B:I.142, B:A.238, B:Y.239 Hydrogen bonds: B:N.138, B:D.141, B:D.141, B:D.141, B:I.142, B:T.248 Salt bridges: B:R.169, B:H.193 P8V.16: 20 residues within 4Å: Chain C: R.106, 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, I.326 Ligands: NAI.15 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:V.110, C:N.138, C:P.139, C:P.139, C:A.238, C:Y.239 Hydrogen bonds: C:N.138, C:D.141, C:D.141, C:I.142, C:E.192, C:T.248, C:T.248 Salt bridges: C:R.169, C:H.193 P8V.19: 20 residues within 4Å: Chain D: R.106, 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, I.326 Ligands: NAI.18 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: 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:I.142, D:E.192, D:T.248, D:T.248 Salt bridges: D:R.169, D:H.193

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

EDO.3: 3 residues within 4Å: Chain A: H.231, K.232, E.236 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.231, A:E.236 EDO.4: 4 residues within 4Å: Chain A: R.106, Y.239, I.242 Ligands: P8V.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.106 EDO.5: 2 residues within 4Å: Chain A: P.122, N.123 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.123 EDO.6: 3 residues within 4Å: Chain A: E.261, R.269 Chain D: L.183 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:D.258, A:R.269, A:R.269 Water bridges: A:K.42, A:K.42, A:K.42, A:D.258, C:F.71 EDO.7: 6 residues within 4Å: Chain A: N.11, L.13, E.15 Chain B: R.268, S.301, D.302 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.268, B:R.268, B:S.301, A:N.11, A:E.15 EDO.10: 3 residues within 4Å: Chain B: H.231, K.232, E.236 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.231, B:E.236 EDO.11: 4 residues within 4Å: Chain B: R.106, Y.239, I.242 Ligands: P8V.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.106 EDO.12: 2 residues within 4Å: Chain B: P.122, N.123 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.123 EDO.13: 3 residues within 4Å: Chain B: E.261, R.269 Chain C: L.183 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain B Water bridges: D:F.71, B:K.42, B:K.42, B:K.42, B:D.258 Hydrogen bonds: B:D.258, B:R.269, B:R.269 EDO.14: 6 residues within 4Å: Chain A: R.268, S.301, D.302 Chain B: N.11, L.13, E.15 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:N.11, B:E.15, A:R.268, A:R.268, A:S.301 EDO.17: 7 residues within 4Å: Chain B: S.202, G.208 Chain C: S.202, G.203, N.205, G.208, S.210 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.202, C:G.208 Water bridges: C:S.210, C:L.211, C:T.213 EDO.20: 7 residues within 4Å: Chain A: S.202, G.208 Chain D: S.202, G.203, N.205, G.208, S.210 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.202, D:G.208 Water bridges: D:S.210, D:L.211, D:T.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rai, G. et al., Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties. J.Med.Chem. (2020)

Release Date

2020-09-23

Peptides

L-lactate dehydrogenase A chain: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
D

C
B

D
B

L-lactate dehydrogenase A chain

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