SMTL ID : 4jnk.1

Lactate Dehydrogenase A in complex with inhibitor compound 22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 24 residues within 4Å: Chain A: V.25, G.28, A.29, V.30, D.51, V.52, I.53, T.94, A.95, G.96, A.97, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: ZHK.3 13 PLIP interactions: 13 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.98 Salt bridges: A:R.98, A:R.98 NAI.5: 27 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, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: LAC.7 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:V.30, B:I.251, 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:K.56, B:R.98, B:R.98, B:Q.99 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.8: 21 residues within 4Å: Chain C: V.25, 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, L.164, H.192, T.247, I.251 Ligands: ZHK.10 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:A.29, C:V.30, C:V.52, C:G.96, C:V.135, C:N.137, C:N.137 Water bridges: C:G.28, C:G.31, C:Y.82, C:R.98, C:R.98, C:R.98, C:R.98, C:R.98 Salt bridges: C:R.98 NAI.12: 24 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, G.96, R.98, I.115, I.119, V.135, S.136, N.137, V.139, S.160, L.164, H.192, T.247, I.251 Ligands: ZHK.13 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.28, D:A.29, D:V.30, D:V.52, D:G.96, D:V.135, D:N.137, D:N.137 Water bridges: D:G.31, D:Y.82, D:N.137 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 ZHK: (2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide(Non-covalent)

ZHK.3: 18 residues within 4Å: Chain A: A.97, R.98, R.105, L.108, V.109, N.137, P.138, V.139, D.140, I.141, E.191, H.192, D.194, A.237, Y.238, I.241, L.322 Ligands: NAI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.108, A:N.137, A:A.237, A:Y.238 Hydrogen bonds: A:N.137, A:D.140, A:D.140, A:I.141, A:E.191, A:D.194 pi-Cation interactions: A:R.105 ZHK.10: 15 residues within 4Å: Chain C: R.105, L.108, V.109, N.137, P.138, V.139, D.140, I.141, E.191, H.192, D.194, Y.238, I.241, L.322 Ligands: NAI.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.238 Hydrogen bonds: C:N.137, C:D.140, C:I.141, C:E.191, C:D.194 Water bridges: C:R.105, C:Y.238 pi-Cation interactions: C:R.105 Halogen bonds: C:R.105 ZHK.13: 16 residues within 4Å: Chain D: A.97, Q.99, R.105, L.108, N.137, P.138, V.139, D.140, I.141, E.191, H.192, D.194, Y.238, I.241, L.322 Ligands: NAI.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.238 Hydrogen bonds: D:Q.99, D:R.105, D:D.140, D:I.141, D:E.191, D:E.191, D:D.194 Water bridges: D:N.137

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

SO4.4: 5 residues within 4Å: Chain A: R.170, H.185 Chain C: L.182, S.183, H.185 11 PLIP interactions: 4 interactions with chain C, 7 interactions with chain A Water bridges: C:L.182, C:H.185, C:A.206, A:R.170, A:R.170, A:R.170, A:V.269, A:V.269 Salt bridges: C:H.185, A:R.170, A:H.185 SO4.11: 5 residues within 4Å: Chain A: L.182, S.183, H.185 Chain C: R.170, H.185 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain A Water bridges: C:R.170, C:R.170, C:R.170, C:R.170, C:R.170, A:A.206 Salt bridges: C:R.170, C:H.185, A:H.185 Hydrogen bonds: A:L.182 SO4.14: 5 residues within 4Å: Chain B: L.182, S.183, H.185 Chain D: R.170, H.185 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain D Water bridges: B:H.185, B:H.185, B:A.206, D:R.170, D:R.170 Salt bridges: B:H.185, D:R.170, D:H.185

1 x LAC: LACTIC ACID(Non-covalent)

LAC.7: 9 residues within 4Å: Chain B: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.5 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.105, B:N.137, B:H.192, 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

Dragovich, P.S. et al., Identification of substituted 2-thio-6-oxo-1,6-dihydropyrimidines as inhibitors of human lactate dehydrogenase. Bioorg.Med.Chem.Lett. (2013)

Release Date

2013-05-22

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