SMTL ID : 6q0d.1 (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

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

PO4.1: 5 residues within 4Å: Chain A: R.171, H.186, W.188 Chain C: S.184, H.186 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Water bridges: C:H.186, A:R.171, A:R.171, A:H.186 Salt bridges: C:H.186, A:R.171, A:H.186 PO4.5: 4 residues within 4Å: Chain B: R.171, H.186 Chain D: S.184, H.186 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain D Water bridges: B:R.171, B:R.171, B:W.188, D:A.207 Salt bridges: B:R.171, B:H.186, D:H.186 Hydrogen bonds: D:L.183 PO4.9: 5 residues within 4Å: Chain A: L.183, S.184, H.186 Chain C: R.171, H.186 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:L.183 Water bridges: A:A.207, C:R.171, C:W.188, C:R.269, C:R.269 Salt bridges: A:H.186, C:R.171, C:H.186 PO4.12: 5 residues within 4Å: Chain B: L.183, S.184, H.186 Chain D: R.171, H.186 8 PLIP interactions: 4 interactions with chain D, 4 interactions with chain B Water bridges: D:R.171, D:W.188, B:L.183, B:A.207 Salt bridges: D:R.171, D:H.186, B:H.186 Hydrogen bonds: B:L.183

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.2: 20 residues within 4Å: Chain A: R.106, 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, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:R.106, A:L.109, A:N.138, A:P.139, A:P.139, A:I.142, 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 Halogen bonds: A:R.106 P8M.6: 20 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, A.238, Y.239, I.242, T.248, L.323, I.326 Ligands: NAI.7 21 PLIP interactions: 21 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:D.141, B:I.142, B:E.192, B:E.192, B:T.248, B:T.248 Salt bridges: B:R.169, B:H.193 Halogen bonds: B:R.106 P8M.10: 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.11 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:R.106, C:R.106, C:L.107, C:V.110, C:N.138, C:P.139, C:P.139, C:A.238, C:Y.239, C:I.326 Hydrogen bonds: C:N.138, C:D.141, C:I.142, C:E.192, C:T.248 Salt bridges: C:R.169, C:H.193 P8M.13: 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.14 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:R.106, D:L.109, D:V.110, D:N.138, D:P.139, D:P.139, D:A.238, D:Y.239, D:I.326 Hydrogen bonds: D:N.138, D:D.141, D:I.142, D:E.192, D:T.248, D:T.248 Salt bridges: D:R.169, D:H.193 pi-Cation interactions: D:R.106 Halogen bonds: D:R.106

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

NAI.3: 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.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.165, A:I.252, A:I.252, A:I.252 Hydrogen bonds: 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 Salt bridges: A:R.99 NAI.7: 24 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, L.165, H.193, T.248, I.252 Ligands: P8M.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.165, B:I.252, B:I.252, B:I.252 Hydrogen bonds: B:V.28, 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.29, B:G.32 Salt bridges: B:R.99 NAI.11: 24 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, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: P8M.10 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:L.165, C:I.252, C:I.252, C:I.252 Hydrogen bonds: C:G.29, C:A.30, C:V.31, C:V.53, C:G.97, C:I.116, 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:R.99 Salt bridges: C:R.99 NAI.14: 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.13 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:G.29, 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.32, D:R.99, D:R.99 Salt bridges: D:R.99

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain B: S.79, G.80, K.81 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.81 Water bridges: B:S.79 GOL.8: 5 residues within 4Å: Chain C: E.55, S.79, G.80, K.81, D.82 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.81, C:D.82 Water bridges: C:S.79

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
B

C
C

D
D

L-lactate dehydrogenase A chain

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