SMTL ID : 4aje.1

rat LDHA in complex with 2-(4-bromophenoxy)propanedioic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x 2B4: 2-(4-BROMANYLPHENOXY)PROPANEDIOIC ACID(Non-covalent)

2B4.1: 13 residues within 4Å: Chain A: V.30, T.94, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247 Ligands: MLI.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.30, A:V.135 Hydrogen bonds: A:Q.99, A:N.137, A:T.247 Water bridges: A:N.137, A:A.237, A:T.247 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 Halogen bonds: A:T.94 2B4.6: 14 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 14 PLIP interactions: 14 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 Water bridges: B:R.105, B:N.137 Salt bridges: B:R.105, B:R.105, B:R.168, B:H.192, B:H.192 Halogen bonds: B:T.94 2B4.9: 14 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 15 PLIP interactions: 15 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:N.137, C:T.247, C:T.247 Salt bridges: C:R.105, C:R.105, C:R.168, C:H.192, C:H.192 Halogen bonds: C:T.94 2B4.12: 12 residues within 4Å: Chain D: V.30, T.94, Q.99, R.105, V.135, S.136, N.137, L.164, R.168, H.192, A.237, T.247 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:V.30 Hydrogen bonds: D:N.137, D:T.247 Salt bridges: D:R.105, D:R.105, D:R.168, D:H.192, D:H.192 Halogen bonds: D:T.94

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

MLI.2: 9 residues within 4Å: Chain A: R.105, N.137, L.164, R.168, H.192, A.237, T.247, I.251 Ligands: 2B4.1 10 PLIP interactions: 10 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 Salt bridges: A:R.105, A:R.105, A:R.168, A:H.192, A:H.192 MLI.3: 8 residues within 4Å: Chain A: R.170, H.185, W.187, V.269 Chain D: L.182, S.183, H.185 Ligands: MLI.4 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Water bridges: A:R.170, A:V.269, D:A.206 Salt bridges: A:R.170, A:H.185, D:H.185, D:H.185 MLI.4: 8 residues within 4Å: Chain A: L.182, S.183, H.185 Chain D: R.170, H.185, W.187, V.269 Ligands: MLI.3 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain D Salt bridges: A:H.185, A:H.185, D:R.170, D:H.185 Hydrophobic interactions: D:W.187 Water bridges: D:R.170, D:H.185 MLI.7: 6 residues within 4Å: Chain B: R.170, H.185, W.187, V.269 Chain C: S.183, H.185 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:V.269 Water bridges: B:R.170, B:H.185 Salt bridges: B:R.170, B:H.185, C:H.185, C:H.185 MLI.10: 7 residues within 4Å: Chain B: L.182, S.183, H.185 Chain C: R.170, H.185, W.187, V.269 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Water bridges: B:A.206 Salt bridges: B:H.185, B:H.185, C:R.170, C:H.185

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain B: G.28, A.29, R.98, Y.246 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.29, B:R.98, B:R.98 Water bridges: B:R.98 GOL.8: 2 residues within 4Å: Chain C: S.104, N.107 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.104, C:N.107 Water bridges: C:S.104, C:D.194 GOL.11: 7 residues within 4Å: Chain C: M.40, K.41 Chain D: M.40, D.42, F.70, L.71, K.72 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:M.40, D:D.42, D:D.42 Water bridges: D:D.42

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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