SMTL ID : 4mp2.1

Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x PV1: (5-bromo-2,4-dihydroxyphenyl)(1,3-dihydro-2H-isoindol-2-yl)methanone(Non-covalent)

PV1.1: 13 residues within 4Å: Chain A: L.245, N.248, A.249, R.251, A.252, E.255, D.283, G.287, V.288, L.296, L.323, L.339, T.347 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.248, A:R.251, A:A.252 Hydrogen bonds: A:N.248, A:D.283, A:G.287 Water bridges: A:G.285, A:T.347 PV1.3: 13 residues within 4Å: Chain B: L.245, N.248, A.249, R.251, A.252, E.255, D.283, G.287, V.288, L.296, L.323, L.339, T.347 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:N.248, B:R.251, B:A.252 Hydrogen bonds: B:N.248, B:D.283, B:G.287 Water bridges: B:G.285, B:T.347

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 5 residues within 4Å: Chain A: E.255, S.256, H.257, E.258, S.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.255, A:E.255, A:E.258, A:S.259 TLA.4: 5 residues within 4Å: Chain B: E.255, S.256, H.257, E.258, S.259 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.255, B:E.255, B:E.258, B:S.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tso, S.C. et al., Structure-guided Development of Specific Pyruvate Dehydrogenase Kinase Inhibitors Targeting the ATP-binding Pocket. J.Biol.Chem. (2014)

Release Date

2014-01-01

Peptides

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

[Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial

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