SMTL ID : 6q13.1 (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: 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: P8V.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: 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, A:S.161 Water bridges: A:G.32, A:R.99 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: P8V.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252, 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:N.138 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: P8V.14 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.252, C:I.252 Hydrogen bonds: C:V.28, C:G.29, 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.32, C:R.99 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: P8V.20 20 PLIP interactions: 20 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:Y.83, D:Y.83, D:R.99, D:N.138 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: 23 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, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.1, EDO.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.106, A:L.109, A:V.110, A:N.138, A:P.139, A:I.142, A:A.238, A:Y.239 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 P8V.8: 22 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, I.326 Ligands: NAI.7, EDO.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: 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:I.142, B:E.192, B:T.248 Salt bridges: B:R.169, B:H.193 pi-Cation interactions: B:R.106 P8V.14: 23 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, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.13, EDO.15 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:R.106, C:L.109, C:V.110, C:N.138, C:P.139, C:I.142, 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 Salt bridges: C:R.169, C:H.193 P8V.20: 22 residues within 4Å: Chain D: 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, I.326 Ligands: NAI.19, EDO.21 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: 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:I.142, D:E.192, D:T.248 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: 4 residues within 4Å: Chain A: R.106, Y.239, I.242 Ligands: P8V.2 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: E.176 Chain B: P.75, K.76 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Q.233, E.240 Chain B: K.59, M.63 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: S.202, G.203, M.204, N.205, G.208, S.210 Chain D: S.202, G.208 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain B: Y.239, I.242 Ligands: P8V.8 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain B: L.173, E.176, R.177 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: V.200, W.201, S.202, T.309, E.312 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: W.148, G.152, F.153, P.154, K.155 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: R.106, Y.239, I.242 Ligands: P8V.14 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: E.176 Chain D: P.75, K.76 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: Q.233, E.240 Chain D: K.59, M.63 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: S.202, G.208 Chain C: S.202, G.203, M.204, N.205, G.208, S.210 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain D: Y.239, I.242 Ligands: P8V.20 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain D: L.173, E.176, R.177 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain D: V.200, W.201, S.202, T.309, E.312 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain D: W.148, G.152, F.153, P.154, K.155 Ligand excluded by PLIP

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
A

B
C

C
A

D
C

L-lactate dehydrogenase A chain

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