SMTL ID : 5w8h.1

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

7 x 9Y1: 2-[3-(4-fluorophenyl)-5-(trifluoromethyl)-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid(Non-covalent)(Non-functional Binders)

9Y1.1: 13 residues within 4Å: Chain A: Q.100, R.106, L.109, N.138, P.139, L.165, R.169, H.193, G.194, D.195, Y.239, T.248, I.252 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.109, A:N.138, A:P.139 Hydrogen bonds: A:N.138 Water bridges: A:D.166, A:R.169 Salt bridges: A:R.169, A:H.193 9Y1.2: 10 residues within 4Å: Chain A: V.26, G.27, V.51, D.52, V.53, Y.83, A.96, I.116, F.119, I.120 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.53, A:V.53, A:A.96, A:I.120 Water bridges: A:N.115 Halogen bonds: A:V.51 9Y1.7: 5 residues within 4Å: Chain B: S.310, E.311, A.314, R.315, K.318 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:E.311, B:A.314, B:R.315, B:K.318 Hydrogen bonds: B:S.310 Water bridges: B:S.310 9Y1.10: 11 residues within 4Å: Chain C: Q.100, L.109, N.138, P.139, R.169, H.193, G.194, D.195, A.238, Y.239, T.248 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.138, C:P.139 Hydrogen bonds: C:N.138 Salt bridges: C:R.169, C:H.193 9Y1.11: 10 residues within 4Å: Chain C: V.26, G.27, V.51, D.52, V.53, A.96, N.115, I.116, F.119, I.120 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.53, C:V.53, C:A.96, C:I.120 Water bridges: C:N.115, C:N.115 Halogen bonds: C:V.51 9Y1.12: 9 residues within 4Å: Chain C: S.105, R.106, L.107, D.321, T.322, G.325, I.326, E.329 Ligands: 9Y1.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.106, C:L.107 Water bridges: C:S.105 9Y1.13: 1 residues within 4Å: Ligands: 9Y1.12 No protein-ligand interaction detected (PLIP)

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: R.171, H.186 Chain C: H.186 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:A.207 Salt bridges: C:H.186, A:R.171, A:H.186 ACT.4: 3 residues within 4Å: Chain A: L.183, H.186 Chain C: R.171 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:L.183 Water bridges: A:A.207, C:R.171 Salt bridges: A:H.186, C:R.171, C:H.186 ACT.8: 4 residues within 4Å: Chain B: D.221, K.222, D.223, Q.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.223 ACT.15: 5 residues within 4Å: Chain D: Y.281, V.306, T.307, L.308, E.313 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.306, D:L.308

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 3 residues within 4Å: Chain A: T.213, L.214 Chain C: T.307 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.214 DMS.9: 6 residues within 4Å: Chain A: L.70 Chain B: N.164, S.167, R.171, V.270, P.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.171 pi-Cation interactions: B:W.188 DMS.16: 4 residues within 4Å: Chain D: G.97, A.98, S.137, N.138 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.138

1 x MLA: MALONIC ACID(Non-covalent)

MLA.6: 7 residues within 4Å: Chain B: R.106, N.138, L.165, R.169, H.193, A.238, T.248 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.165 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

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 12 residues within 4Å: Chain A: S.202, G.203, M.204, N.205, G.208, S.210 Chain C: S.202, G.203, M.204, N.205, G.208, S.210 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:G.203, A:N.205, A:G.208, C:M.204, C:N.205 Water bridges: A:S.210, A:L.211, C:S.210, C:L.211 GOL.17: 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 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:M.204, D:G.203, D:G.208 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
A

B
B

C
C

D
D

L-lactate dehydrogenase A chain

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