SMTL ID : 4i9n.1 (1 other biounit)

Crystal structure of rabbit LDHA in complex with AP28161 and AP28122

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x 1E6: 6-({2-[(5-chloro-4-{[(2S)-2,3-dihydroxypropyl]oxy}-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid(Non-covalent)

1E6.1: 15 residues within 4Å: Chain A: V.25, G.26, V.27, G.28, D.51, V.52, T.94, A.95, G.96, R.111, N.114, I.115, F.118, I.119 Ligands: 1E5.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.52, A:N.114, A:I.115, A:I.119 Hydrogen bonds: A:V.27, A:D.51, A:G.96 Water bridges: A:Y.82 Salt bridges: A:R.111 1E6.3: 15 residues within 4Å: Chain B: V.25, G.26, V.27, G.28, D.51, V.52, T.94, A.95, G.96, R.111, N.114, I.115, F.118, I.119 Ligands: 1E5.4 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.52, B:I.115, B:I.119 Hydrogen bonds: B:D.51, B:G.96 Salt bridges: B:R.111 1E6.5: 16 residues within 4Å: Chain C: V.25, G.26, V.27, G.28, V.50, D.51, V.52, T.94, A.95, G.96, R.111, N.114, I.115, F.118, I.119 Ligands: 1E5.6 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.52, C:I.115, C:I.119 Hydrogen bonds: C:D.51, C:G.96 Water bridges: C:G.28 Salt bridges: C:R.111 Halogen bonds: C:V.50 1E6.7: 14 residues within 4Å: Chain D: G.26, V.27, G.28, D.51, V.52, T.94, A.95, G.96, R.111, N.114, I.115, F.118, I.119 Ligands: 1E5.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.52, D:N.114, D:I.115 Hydrogen bonds: D:V.27, D:D.51, D:G.96, D:G.96 Salt bridges: D:R.111

4 x 1E5: 6-[3-(carboxymethoxy)-5-fluorophenyl]pyridine-3-carboxylic acid(Non-covalent)

1E5.2: 12 residues within 4Å: Chain A: G.28, A.29, V.30, T.94, V.135, S.136, N.137, L.164, R.168, A.237, T.247 Ligands: 1E6.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.30, A:V.135 Hydrogen bonds: A:A.29, A:V.30 Water bridges: A:G.28, A:G.31, A:D.165, A:D.165, A:H.192 Salt bridges: A:R.168 1E5.4: 13 residues within 4Å: Chain B: G.28, A.29, V.30, I.93, T.94, V.135, S.136, N.137, L.164, R.168, A.237, T.247 Ligands: 1E6.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.30, B:V.30, B:V.135 Hydrogen bonds: B:G.28, B:A.29, B:V.30, B:T.247, B:T.247 Water bridges: B:G.31, B:T.247 Salt bridges: B:R.168 Halogen bonds: B:I.93 1E5.6: 11 residues within 4Å: Chain C: G.28, A.29, V.30, T.94, V.135, S.136, N.137, R.168, A.237, T.247 Ligands: 1E6.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:V.30, C:V.135 Hydrogen bonds: C:G.28, C:A.29, C:V.30, C:T.94, C:T.247 Water bridges: C:G.31 Salt bridges: C:R.168 1E5.8: 12 residues within 4Å: Chain D: G.28, A.29, V.30, T.94, V.135, S.136, N.137, L.164, R.168, A.237, T.247 Ligands: 1E6.7 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.30, D:V.30, D:V.135 Hydrogen bonds: D:G.28, D:A.29, D:V.30, D:T.94, D:N.137 Water bridges: D:G.31, D:G.31, D:H.192, D:H.192 Salt bridges: D:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kohlmann, A. et al., Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors. J.Med.Chem. (2013)

Release Date

2013-01-23

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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