SMTL ID : 4ajj.1

rat LDHA in complex with 2-((3,4-dimethoxyphenyl)methyl))propanedioic acid and N-(2-methyl-1,3-benzothiazol-6-yl)-3-ureido-propanamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x 88S: N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)-3-UREIDO-PROPANAMIDE(Non-covalent)

88S.1: 11 residues within 4Å: Chain A: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.95, A:F.118, A:I.119 Hydrogen bonds: A:D.51, A:G.96, A:G.96, A:G.96 Water bridges: A:G.28, A:V.30 88S.3: 12 residues within 4Å: Chain B: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 Ligands: 88R.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.52, B:A.95, B:F.118, B:I.119 Hydrogen bonds: B:G.28, B:D.51, B:G.96, B:G.96, B:G.96 Water bridges: B:V.30, B:Y.82, B:R.98 88S.7: 12 residues within 4Å: Chain C: G.26, G.28, D.51, V.52, T.94, A.95, G.96, I.115, F.118, I.119 Ligands: DMS.5, 88R.8 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.52, C:A.95, C:F.118, C:I.119 Hydrogen bonds: C:D.51, C:G.96, C:G.96, C:G.96 Water bridges: C:G.28, C:A.29 88S.9: 11 residues within 4Å: Chain D: G.26, G.28, D.51, V.52, T.94, A.95, G.96, R.98, I.115, F.118, I.119 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.52, D:A.95, D:F.118, D:I.119 Hydrogen bonds: D:G.28, D:D.51, D:G.96, D:G.96, D:G.96 Water bridges: D:A.29, D:V.30, D:V.30

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 8 residues within 4Å: Chain A: R.105, N.137, L.164, R.168, H.192, A.237, T.247, I.251 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.164, A:I.251 Hydrogen bonds: A:N.137, A:T.247 Water bridges: A:T.247, A:T.247 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 MLI.10: 8 residues within 4Å: Chain D: Q.99, R.105, N.137, L.164, R.168, H.192, A.237, T.247 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:Q.99, D:N.137, D:T.247 Water bridges: D:N.137, D:H.192, D:T.247 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192

2 x 88R: 2-((3,4-DIMETHOXYPHENYL)METHYL))PROPANEDIOIC ACID(Non-covalent)

88R.4: 15 residues within 4Å: Chain B: V.30, T.94, R.98, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247, I.251 Ligands: 88S.3 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.30, B:V.135, B:I.251 Hydrogen bonds: B:Q.99, B:N.137, B:T.247, B:T.247 Water bridges: B:Q.99 Salt bridges: B:R.105, B:R.105, B:R.168, B:H.192, B:H.192 88R.8: 15 residues within 4Å: Chain C: V.30, T.94, R.98, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247, I.251 Ligands: 88S.7 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.30, C:V.135, C:I.251 Hydrogen bonds: C:Q.99, C:N.137, C:T.247 Water bridges: C:T.247 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192

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

DMS.5: 4 residues within 4Å: Chain C: G.96, A.97, I.115 Ligands: 88S.7 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain B: S.201, G.202, N.204, G.207 Chain C: S.201, G.202, V.203, N.204, G.207, S.209 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.202, B:G.202, B:N.204 Water bridges: C:L.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ward, R. et al., The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation. J.Med.Chem. (2012)

Release Date

2012-03-21

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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