SMTL ID : 5w8k.1

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29 and NADH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

3 x 9Y7: 2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid(Non-covalent)

9Y7.1: 17 residues within 4Å: Chain A: 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, I.242, T.248, L.323 Ligands: NAI.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:N.138 Hydrogen bonds: A:N.138, A:D.141, A:D.141, A:I.142, A:E.192 Water bridges: A:H.193 Salt bridges: A:R.169, A:H.193 9Y7.15: 19 residues within 4Å: Chain C: L.109, V.110, N.113, 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 Ligands: NAI.16 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.109, C:N.138, C:P.139 Hydrogen bonds: C:N.138, C:D.141, C:I.142, C:E.192 Water bridges: C:R.169, C:H.193, C:Y.239 Salt bridges: C:R.169, C:H.193 9Y7.21: 17 residues within 4Å: Chain D: Q.100, L.109, N.138, P.139, V.140, D.141, I.142, L.165, R.169, E.192, H.193, G.194, A.238, I.242, T.248, L.323 Ligands: NAI.22 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.109, D:N.138, D:P.139 Hydrogen bonds: D:N.138, D:D.141, D:I.142, D:E.192, D:E.192, D:T.248, D:T.248 Salt bridges: D:R.169, D:H.193

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

NAI.2: 26 residues within 4Å: Chain A: V.26, G.27, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, A.98, 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: 9Y7.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.252, A:I.252 Hydrogen bonds: A:A.30, A:V.31, A:V.53, A:K.57, A:K.57, A:G.97, A:V.136, A:N.138, A:N.138, A:S.161 Water bridges: A:G.29, A:G.32, A:K.57 Salt bridges: A:K.57, A:R.99, A:R.99 NAI.10: 26 residues within 4Å: Chain B: V.26, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, A.98, R.99, N.113, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: MLA.9 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:V.31, B:I.252, B:I.252 Hydrogen bonds: B:A.30, B:V.31, B:V.53, B:K.57, B:K.57, B:G.97, B:A.98, B:N.113, B:V.136, B:N.138, B:N.138, B:S.161 Water bridges: B:G.29, B:G.32, B:K.57, B:R.99, B:R.99, B:Q.100 Salt bridges: B:K.57, B:R.99, B:R.99 NAI.16: 24 residues within 4Å: Chain C: V.26, G.27, V.28, G.29, A.30, V.31, D.52, V.53, I.54, K.57, T.95, A.96, G.97, I.116, I.120, V.136, S.137, N.138, S.161, L.165, H.193, T.248, I.252 Ligands: 9Y7.15 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:L.165, C:I.252, C:I.252, C:I.252 Hydrogen bonds: C:V.28, C:G.29, C:V.31, C:V.53, C:K.57, C:K.57, C:G.97, C:V.136, C:N.138, C:N.138 Water bridges: C:A.30, C:A.30, C:G.32, C:Y.83 Salt bridges: C:K.57 NAI.22: 23 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, I.116, I.120, V.136, S.137, N.138, V.140, S.161, L.165, H.193, T.248, I.252 Ligands: 9Y7.21 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.252, D:I.252 Hydrogen bonds: D:V.28, D:G.29, D:A.30, D:V.31, D:V.53, D:G.97, D:V.136, D:N.138, D:N.138 Water bridges: D:G.32, D:Y.83, D:Y.83, D:T.95, D:G.97, D:N.138

5 x MLA: MALONIC ACID(Non-covalent)

MLA.3: 6 residues within 4Å: Chain A: R.171, H.186, W.188, V.270 Chain C: S.184, H.186 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Water bridges: A:R.171, A:R.171, A:H.186, A:W.188, C:A.207 Salt bridges: A:R.171, A:H.186, C:H.186, C:H.186 MLA.9: 9 residues within 4Å: Chain B: Q.100, R.106, N.138, L.165, R.169, H.193, A.238, T.248 Ligands: NAI.10 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:A.238, B:T.248 Hydrogen bonds: B:Q.100, B:N.138, B:T.248, B:T.248 Salt bridges: B:R.106, B:R.106, B:R.169, B:H.193, B:H.193 MLA.11: 7 residues within 4Å: Chain B: R.171, H.186, W.188, V.270 Chain D: S.184, H.186 Ligands: GOL.14 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain B Water bridges: D:S.184, D:H.186, B:R.171, B:H.186, B:W.188, B:V.270 Salt bridges: D:H.186, D:H.186, B:R.171, B:H.186 MLA.17: 7 residues within 4Å: Chain A: S.184, H.186 Chain C: R.171, H.186, W.188, V.270 Ligands: GOL.20 9 PLIP interactions: 5 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:W.188 Water bridges: C:R.171, C:H.186, A:H.186, A:A.207 Salt bridges: C:R.171, C:H.186, A:H.186, A:H.186 MLA.23: 6 residues within 4Å: Chain B: S.184, H.186 Chain D: R.171, H.186, W.188, V.270 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain D Water bridges: B:H.186, B:A.207, D:R.171 Salt bridges: B:H.186, B:H.186, D:R.171, D:H.186 Hydrophobic interactions: D:W.188

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 12 residues within 4Å: Chain A: S.202, G.203, M.204, N.205, S.210 Chain C: S.202, G.203, M.204, N.205, G.208, S.210 Ligands: GOL.18 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:G.203, A:N.205, C:M.204 Water bridges: A:S.210, A:L.211, C:S.210, C:L.211 GOL.5: 4 residues within 4Å: Chain A: L.280, Y.281, K.305, V.306 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.281 Water bridges: A:G.279, A:G.282, A:V.306, A:T.307 GOL.6: 5 residues within 4Å: Chain A: Y.172, L.173, E.176 Chain B: M.63, Q.66 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.176 Water bridges: B:Q.66 GOL.7: 7 residues within 4Å: Chain A: M.41, D.43, F.71, L.72, R.73 Chain B: M.41, K.42 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:M.41, A:D.43, A:F.71, A:R.73 Water bridges: B:K.42, A:D.43 GOL.8: 6 residues within 4Å: Chain A: G.282, I.283, K.284, D.285, A.320, D.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.282, A:K.284, A:D.285, A:A.320, A:D.321 GOL.12: 4 residues within 4Å: Chain B: L.280, Y.281, V.306, T.307 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.281 Water bridges: B:G.282, B:L.308 GOL.13: 5 residues within 4Å: Chain B: G.208, V.209, S.210 Chain D: S.202 Ligands: GOL.24 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:S.202, B:S.210 Water bridges: D:S.202, D:S.202, D:S.202, D:T.307, D:T.307, B:T.213 GOL.14: 7 residues within 4Å: Chain A: L.70, F.71 Chain B: R.171, L.183, D.258, R.269 Ligands: MLA.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.171, B:R.171, B:D.258, B:R.269, A:L.70 GOL.18: 5 residues within 4Å: Chain A: S.202 Chain C: G.208, V.209, S.210 Ligands: GOL.4 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.208, C:S.210, A:S.202, A:S.202 Water bridges: A:T.307 GOL.19: 3 residues within 4Å: Chain C: L.280, Y.281, V.306 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.281, C:V.306 GOL.20: 7 residues within 4Å: Chain C: N.164, R.171, H.271, P.272 Chain D: L.70, F.71 Ligands: MLA.17 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.171, C:R.171 Water bridges: C:N.164, C:S.167, C:V.270, C:H.271 GOL.24: 11 residues within 4Å: Chain B: G.203, N.205, G.208, S.210 Chain D: S.202, G.203, M.204, N.205, G.208, S.210 Ligands: GOL.13 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:G.203, B:N.205, D:G.203, D:N.205 Water bridges: B:S.202, B:S.202, B:S.210, D:L.211, D:T.213 GOL.25: 4 residues within 4Å: Chain C: M.63, Q.66 Chain D: Y.172, E.176 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:Q.66 Hydrogen bonds: D:Y.172, D:E.176 GOL.26: 4 residues within 4Å: Chain D: L.280, Y.281, K.305, V.306 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.281, D:V.306 Water bridges: D:G.279, D:G.282

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

Related Entries With Identical Sequence