SMTL ID : 7eat.1

Crystal structure of human pyruvate dehydrogenase kinase 4 in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 2 residues within 4Å: Chain A: R.294, R.298 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.294, A:R.298 SO4.2: 4 residues within 4Å: Chain A: R.117, H.121, R.159, R.163 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.117 Water bridges: A:R.159, A:R.159 Salt bridges: A:H.121, A:R.159, A:R.163 SO4.4: 2 residues within 4Å: Chain B: R.294, R.298 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.294, B:R.298 SO4.5: 5 residues within 4Å: Chain B: R.117, H.121, R.159, R.163, N.167 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.159, B:N.167 Water bridges: B:R.159 Salt bridges: B:H.121, B:R.163

2 x W6P: 1,3-dihydro-2H-indol-2-one(Non-covalent)

W6P.3: 10 residues within 4Å: Chain A: L.248, N.251, A.252, A.255, D.286, V.291, L.299, L.327, L.343, T.351 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.248, A:N.251, A:L.327, A:L.327, A:L.343, A:L.343 Hydrogen bonds: A:D.286, A:T.351 W6P.6: 10 residues within 4Å: Chain B: L.248, N.251, A.252, A.255, D.286, V.291, L.299, L.327, L.343, T.351 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.248, B:N.251, B:L.299, B:L.327, B:L.343 Hydrogen bonds: B:D.286 Water bridges: B:G.290, B:T.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akaki, T. et al., Fragment-based lead discovery to identify novel inhibitors that target the ATP binding site of pyruvate dehydrogenase kinases. Bioorg.Med.Chem. (2021)

Release Date

2021-08-04

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial

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