SMTL ID : 4m49.1

Lactate Dehydrogenase A in complex with a substituted pyrazine inhibitor compound 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 20 residues within 4Å: Chain A: G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, I.115, I.119, V.135, S.136, N.137, S.160, H.192, T.247, I.251 Ligands: 22Y.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.251 Hydrogen bonds: A:A.29, A:V.30, A:V.52, A:G.96, A:V.135, A:N.137, A:N.137 Water bridges: A:G.28, A:G.31, A:R.168 NAI.5: 26 residues within 4Å: Chain B: V.25, G.28, A.29, V.30, D.51, V.52, I.53, K.56, T.94, A.95, G.96, A.97, R.98, Q.99, N.112, I.115, I.119, V.135, S.136, N.137, S.160, L.164, H.192, T.247, I.251 Ligands: LAC.7 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251, B:I.251 Hydrogen bonds: B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, B:G.96, B:G.96, B:A.97, B:N.112, B:V.135, B:N.137, B:N.137, B:S.160 Water bridges: B:G.28, B:G.31, B:R.98, B:R.98 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.8: 21 residues within 4Å: Chain C: G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, H.192, T.247, I.251 Ligands: 22Y.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.247, C:I.251 Hydrogen bonds: C:G.28, C:A.29, C:V.30, C:V.52, C:G.96, C:V.135, C:N.137, C:N.137, C:S.160 Water bridges: C:G.31 NAI.12: 22 residues within 4Å: Chain D: V.25, G.26, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, H.192, T.247, I.251 Ligands: 22Y.13 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.251 Hydrogen bonds: D:G.28, D:V.30, D:V.52, D:Y.82, D:V.135, D:N.137, D:N.137 Water bridges: D:G.31, D:L.164 Salt bridges: D:R.98

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 5 residues within 4Å: Chain A: W.147, G.151, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.154 Salt bridges: A:K.154 EPE.6: 5 residues within 4Å: Chain B: W.147, G.151, F.152, P.153, K.154 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.147, B:K.154 EPE.9: 5 residues within 4Å: Chain C: W.147, G.151, F.152, P.153, K.154 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.154

3 x 22Y: 3-(5-amino-6-{[(1R)-1-phenylethyl]amino}pyrazin-2-yl)-4-chlorobenzoic acid(Non-covalent)

22Y.3: 10 residues within 4Å: Chain A: V.30, R.98, N.137, H.192, A.237, I.241, G.245, Y.246, T.247 Ligands: NAI.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.241 Hydrogen bonds: A:N.137, A:T.247, A:T.247 Salt bridges: A:H.192 22Y.10: 10 residues within 4Å: Chain C: V.30, R.98, N.137, H.192, A.237, I.241, G.245, Y.246, T.247 Ligands: NAI.8 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:R.98, C:A.237, C:I.241 Hydrogen bonds: C:N.137, C:T.247, C:T.247 Salt bridges: C:H.192 pi-Cation interactions: C:R.98 22Y.13: 10 residues within 4Å: Chain D: V.30, R.98, N.137, H.192, A.237, I.241, G.245, Y.246, T.247 Ligands: NAI.12 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:R.98, D:A.237, D:I.241 Hydrogen bonds: D:N.137, D:T.247, D:T.247 Salt bridges: D:H.192

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 4 residues within 4Å: Chain A: R.170, H.185 Chain C: L.182, H.185 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain C Water bridges: A:R.170, A:H.185, C:L.182, C:A.206 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.11: 5 residues within 4Å: Chain A: L.182, S.183, H.185 Chain C: R.170, H.185 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:L.182 Water bridges: A:A.206, C:R.170, C:W.187 Salt bridges: A:H.185, C:R.170, C:H.185 SO4.14: 5 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D Water bridges: B:S.183, B:H.185, B:H.185, B:A.206 Salt bridges: B:H.185, D:R.170, D:H.185

1 x LAC: LACTIC ACID(Non-covalent)

LAC.7: 10 residues within 4Å: Chain B: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, I.241, T.247 Ligands: NAI.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.237 Hydrogen bonds: B:R.105, B:R.105, B:N.137, B:T.247, B:T.247 Salt bridges: B:R.105, B:R.168, B:H.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fauber, B.P. et al., Identification of 2-amino-5-aryl-pyrazines as inhibitors of human lactate dehydrogenase. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-09-04

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