SMTL ID : 4rls.1

Lactate Dehydrogenase in complex with inhibitor compound 47

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-tetramer

Ligands

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

NAI.1: 22 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, R.98, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, H.192, T.247, I.251 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.30, A:I.251 Hydrogen bonds: A:V.27, A:A.29, A:V.30, A:V.52, A:Y.82, A:T.94, A:G.96, A:V.135, A:N.137, A:N.137, A:S.160 Water bridges: A:G.31, A:Y.82 Salt bridges: A:R.98 NAI.3: 28 residues within 4Å: Chain B: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, K.56, Y.82, T.94, A.95, G.96, A.97, R.98, I.115, F.118, I.119, V.135, S.136, N.137, V.139, S.160, H.192, T.247, I.251 Ligands: 2OP.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.30, B:V.135, B:I.251 Hydrogen bonds: B:V.27, B:A.29, B:V.30, B:V.52, B:K.56, B:K.56, 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 Salt bridges: B:K.56, B:R.98, B:R.98 NAI.5: 20 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, I.251 Ligands: 2OP.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:V.135, C:I.251 Hydrogen bonds: C:A.29, C:V.30, C:V.52, C:G.96, C:V.135, C:N.137, C:N.137, C:N.137, C:S.160 Water bridges: C:G.28, C:R.98, C:R.98, C:L.164 Salt bridges: C:R.98, C:R.98 NAI.8: 25 residues within 4Å: Chain D: V.25, G.26, V.27, G.28, A.29, V.30, D.51, V.52, I.53, Y.82, T.94, A.95, G.96, A.97, R.98, I.115, F.118, I.119, V.135, S.136, N.137, S.160, H.192, I.251 Ligands: 49C.9 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:V.30, D:V.135, D:I.251, D:I.251, D:I.251 Hydrogen bonds: D:V.27, D:A.29, D:V.30, D:V.52, D:G.96, D:A.97, D:V.135, D:N.137, D:N.137, D:S.160 Water bridges: D:G.28, D:G.28, D:Y.82

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

SO4.2: 6 residues within 4Å: Chain A: R.170, H.185, W.187 Chain C: L.182, S.183, H.185 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Water bridges: A:R.170, A:W.187, A:V.269, C:H.185 Salt bridges: A:R.170, A:H.185, C:H.185 SO4.6: 3 residues within 4Å: Chain A: H.185 Chain C: R.170, H.185 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:L.182 Water bridges: A:H.185, A:A.206, C:R.170, C:R.170, C:R.170, C:H.185 Salt bridges: A:H.185, C:R.170, C:H.185

2 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.4: 7 residues within 4Å: Chain B: N.137, L.164, R.168, H.192, A.237, T.247 Ligands: NAI.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.137, B:T.247, B:T.247, B:T.247 Salt bridges: B:R.168, B:H.192 2OP.7: 6 residues within 4Å: Chain C: N.137, R.168, H.192, A.237, T.247 Ligands: NAI.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.137, C:T.247 Salt bridges: C:R.168, C:H.192

1 x 49C: (1R)-5'-[(2-chlorophenyl)sulfanyl]-4'-hydroxy-2,3-dihydrospiro[indene-1,2'-pyran]-6'(3'H)-one(Non-covalent)

49C.9: 14 residues within 4Å: Chain D: R.98, N.137, L.164, D.165, R.168, H.192, G.193, V.233, V.234, A.237, I.241, Y.246, T.247 Ligands: NAI.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:R.98, D:A.237, D:I.241, D:Y.246 Hydrogen bonds: D:N.137, D:N.137, D:T.247 Salt bridges: D:R.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fauber, B.P. et al., Identification of 3,6-disubstituted dihydropyrones as inhibitors of human lactate dehydrogenase. Bioorg.Med.Chem.Lett. (2014)

Release Date

2014-11-12

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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