- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)
ZN.1: 2 residues within 4Å:- Chain A: H.193
- Ligands: 9YD.3
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.193, H2O.8
ZN.2: 2 residues within 4Å:- Ligands: CIT.4, CIT.12
No protein-ligand interaction detected (PLIP)ZN.10: 2 residues within 4Å:- Chain C: H.193
- Ligands: 9YD.11
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:H.193, H2O.25
ZN.14: 2 residues within 4Å:- Ligands: CIT.7, CIT.17
No protein-ligand interaction detected (PLIP)ZN.15: 2 residues within 4Å:- Chain D: H.193
- Ligands: 9YD.16
2 PLIP interactions:1 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:H.193, H2O.34
- 3 x 9YD: 2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid(Non-covalent)
9YD.3: 11 residues within 4Å:- Chain A: Q.100, R.106, L.109, N.138, L.165, R.169, H.193, A.238, T.248, I.252
- Ligands: ZN.1
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:Q.100, A:L.109, A:N.138
- Salt bridges: A:R.169, A:H.193
9YD.11: 10 residues within 4Å:- Chain C: Q.100, R.106, L.109, N.138, R.169, H.193, A.238, T.248, I.252
- Ligands: ZN.10
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:Q.100, C:L.109, C:N.138
- Salt bridges: C:R.169, C:H.193
9YD.16: 11 residues within 4Å:- Chain D: A.98, Q.100, L.109, N.138, L.165, R.169, H.193, A.238, T.248, I.252
- Ligands: ZN.15
8 PLIP interactions:8 interactions with chain D- Hydrophobic interactions: D:N.138
- Hydrogen bonds: D:T.248, D:T.248
- Water bridges: D:H.193, D:H.193, D:A.238
- Salt bridges: D:R.169, D:H.193
- 4 x CIT: CITRIC ACID(Non-functional Binders)
CIT.4: 12 residues within 4Å:- Chain A: R.171, L.183, H.186, W.188, R.269, V.270
- Chain B: L.70
- Chain C: L.183, S.184, H.186
- Ligands: ZN.2, CIT.12
9 PLIP interactions:2 interactions with chain D, 6 interactions with chain A, 1 interactions with chain C- Water bridges: D:R.73, A:H.186, A:R.269, A:R.269
- Salt bridges: D:R.73, A:R.171, A:H.186, A:R.269, C:H.186
CIT.7: 10 residues within 4Å:- Chain B: R.171, L.183, H.186, R.269, V.270
- Chain D: L.183, S.184, H.186
- Ligands: ZN.14, CIT.17
11 PLIP interactions:8 interactions with chain B, 2 interactions with chain C, 1 interactions with chain D- Water bridges: B:H.186, B:R.269, B:R.269, B:R.269, B:V.270, C:R.73
- Salt bridges: B:R.171, B:H.186, B:R.269, C:R.73, D:H.186
CIT.12: 12 residues within 4Å:- Chain A: L.183, S.184, H.186
- Chain C: R.171, L.183, H.186, W.188, R.269, V.270
- Chain D: L.70
- Ligands: ZN.2, CIT.4
10 PLIP interactions:6 interactions with chain C, 2 interactions with chain A, 2 interactions with chain B- Water bridges: C:H.186, C:R.269, C:R.269, A:H.186, B:R.73
- Salt bridges: C:R.171, C:H.186, C:R.269, A:H.186, B:R.73
CIT.17: 11 residues within 4Å:- Chain B: L.183, S.184, H.186
- Chain D: R.171, L.183, H.186, W.188, R.269, V.270
- Ligands: CIT.7, ZN.14
10 PLIP interactions:6 interactions with chain D, 2 interactions with chain B, 2 interactions with chain A- Water bridges: D:H.186, D:R.269, D:R.269, A:R.73
- Salt bridges: D:R.171, D:H.186, D:R.269, B:H.186, A:R.73
- Hydrogen bonds: B:L.183
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.5: 5 residues within 4Å:- Chain A: N.164, S.167, R.171, P.272
- Chain B: L.70
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.171
- pi-Cation interactions: A:W.188
DMS.8: 7 residues within 4Å:- Chain A: L.70
- Chain B: N.164, S.167, R.171, W.188, V.270, P.272
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.171
- pi-Cation interactions: B:W.188
DMS.13: 7 residues within 4Å:- Chain C: N.164, S.167, R.171, W.188, V.270, P.272
- Chain D: L.70
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:R.171
- pi-Cation interactions: C:W.188
DMS.18: 6 residues within 4Å:- Chain C: L.70
- Chain D: N.164, S.167, R.171, V.270, P.272
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:R.171
- Water bridges: D:G.187
- pi-Cation interactions: D:W.188
- 1 x MLA: MALONIC ACID(Non-covalent)
MLA.6: 8 residues within 4Å:- Chain B: R.106, N.138, L.165, R.169, H.193, A.238, T.248, I.252
11 PLIP interactions:11 interactions with chain B- Hydrophobic interactions: B:L.165, B:I.252
- 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
- 1 x GOL: GLYCEROL(Non-functional Binders)
GOL.9: 12 residues within 4Å:- Chain B: S.202, G.203, M.204, N.205, G.208, S.210
- Chain D: S.202, G.203, M.204, N.205, G.208, S.210
5 PLIP interactions:2 interactions with chain B, 3 interactions with chain D- Hydrogen bonds: B:M.204, D:G.203
- Water bridges: B:M.204, D:S.210, D:L.211
- 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- homo-tetramer
- Ligands
- 5 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)
- 3 x 9YD: 2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid(Non-covalent)
- 4 x CIT: CITRIC ACID(Non-functional Binders)
- 4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x MLA: MALONIC ACID(Non-covalent)
- 1 x GOL: GLYCEROL(Non-functional Binders)
- 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
AB
BC
CD
D