SMTL ID : 6q0d.2 (1 other biounit)

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: V.198, P.199, W.201, T.309, E.311, E.312, R.315 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.199, A:T.309, A:E.311 GOL.2: 1 residues within 4Å: Chain A: K.42 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.42 Water bridges: A:E.261, A:E.261, C:F.71 GOL.3: 5 residues within 4Å: Chain A: D.6, I.9, Y.10, N.11 Chain B: K.305 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.6, A:N.11, B:K.305 GOL.7: 2 residues within 4Å: Chain B: A.314, K.317 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain C: V.198, P.199, W.201, T.309, E.311, E.312, R.315 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:P.199, C:E.311, C:E.311, C:E.312 GOL.12: 1 residues within 4Å: Chain C: K.42 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:K.42 Water bridges: C:E.261, A:F.71 GOL.13: 5 residues within 4Å: Chain C: D.6, I.9, Y.10, N.11 Chain D: K.305 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.6, C:N.11, D:K.305 GOL.17: 2 residues within 4Å: Chain D: A.314, K.317 No protein-ligand interaction detected (PLIP)

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 5 residues within 4Å: Chain A: R.171, H.186 Chain D: L.183, S.184, H.186 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Water bridges: A:R.171, A:R.171, D:A.207 Salt bridges: A:R.171, A:H.186, D:H.186 Hydrogen bonds: D:L.183 PO4.8: 5 residues within 4Å: Chain B: R.171, H.186, W.188 Chain C: S.184, H.186 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Water bridges: C:H.186, C:A.207, B:R.171, B:R.171, B:R.171, B:H.186, B:V.270 Salt bridges: C:H.186, B:R.171, B:H.186 PO4.14: 5 residues within 4Å: Chain B: L.183, S.184, H.186 Chain C: R.171, H.186 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:L.183 Water bridges: B:A.207, C:R.171, C:R.171, C:H.186 Salt bridges: B:H.186, C:R.171, C:H.186 PO4.18: 5 residues within 4Å: Chain A: S.184, H.186 Chain D: R.171, H.186, W.188 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain D Water bridges: A:H.186, A:A.207, D:R.171, D:R.171, D:R.171, D:V.270 Salt bridges: A:H.186, D:R.171, D:H.186

4 x P8M: 2-{3-[3-(cyclopentylethynyl)-4-fluorophenyl]-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid(Non-covalent)

P8M.5: 21 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, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.6 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:R.106, A:R.106, A:L.107, A:L.109, A:V.110, A:V.110, A:N.138, A:P.139, A:I.142, A:A.238, A:Y.239, 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 P8M.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, I.326 Ligands: NAI.10 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.106, B:L.109, B:N.138, B:P.139, B:P.139, B:I.142, B:A.238, B:Y.239, B:Y.239, B:I.326 Hydrogen bonds: B:N.138, B:D.141, B:I.142, B:E.192, B:E.192, B:T.248, B:T.248 Water bridges: B:R.169 Salt bridges: B:R.169, B:H.193 P8M.15: 21 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, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.16 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:R.106, C:R.106, C:L.107, C:L.109, C:V.110, C:V.110, C:N.138, C:P.139, C:I.142, C:A.238, C:Y.239, C:Y.239, C:I.326 Hydrogen bonds: C:N.138, C:D.141, C:I.142, C:E.192, C:E.192, C:T.248, C:T.248 Salt bridges: C:R.169, C:H.193 P8M.19: 21 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.20 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:R.106, D:L.109, D:N.138, D:P.139, D:P.139, D:I.142, D:A.238, D:Y.239, D:Y.239, D:I.326 Hydrogen bonds: D:N.138, D:D.141, D:D.141, D:I.142, D:E.192, D:T.248 Water bridges: D:R.169 Salt bridges: D:R.169, D:H.193

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

NAI.6: 25 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, 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: P8M.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.165, A:I.252, A:I.252, A:I.252 Hydrogen bonds: 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:V.28, A:G.29, A:G.32, A:R.99, A:R.99 Salt bridges: A:R.99 NAI.10: 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: P8M.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252, B:I.252, B:I.252 Hydrogen bonds: 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, B:K.57 Salt bridges: B:R.99 NAI.16: 25 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, 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: P8M.15 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:L.165, C:I.252, C:I.252, C:I.252 Hydrogen bonds: 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:V.28, C:G.29, C:G.32, C:R.99, C:R.99 Salt bridges: C:R.99 NAI.20: 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: P8M.19 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.165, D:I.252, D:I.252, D:I.252 Hydrogen bonds: D:A.30, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138, D:S.161 Water bridges: D:G.29, D:G.32, D:K.57 Salt bridges: D:R.99

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
E

B
F

C
E

D
F

L-lactate dehydrogenase A chain

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