SMTL ID : 6lin.1 (1 other biounit)

Crystal structure of human PDK2 complexed with GM10030

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.323, K.324, R.327 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.323, A:K.324, A:R.327 SO4.4: 4 residues within 4Å: Chain B: R.191, N.195, H.272, Y.361 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.195, B:N.195, B:Y.361 Salt bridges: B:R.191, B:H.272

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.191, N.195, S.268, H.272 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.191, A:R.191, A:S.268, A:S.268

2 x EH0: 4-[[[4-[3,5-bis(fluoranyl)-4-(4-oxidanyl-4-oxidanylidene-butoxy)phenyl]-5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]benzoic acid(Non-covalent)

EH0.3: 20 residues within 4Å: Chain A: L.277, N.280, A.281, R.283, A.284, D.315, G.317, G.319, V.320, P.321, K.324, R.327, L.328, S.330, Y.333, G.352, L.355, L.371, E.375, T.379 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.280, A:V.320, A:K.324, A:T.379 Hydrogen bonds: A:N.280, A:D.315, A:G.319, A:T.379 Water bridges: A:L.277, A:G.317 Salt bridges: A:K.324 EH0.5: 17 residues within 4Å: Chain B: L.277, N.280, A.281, R.283, A.284, D.315, G.319, V.320, P.321, K.324, L.328, Y.333, G.352, G.354, L.355, L.371, T.379 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:N.280, B:A.284, B:V.320, B:L.328, B:T.379 Hydrogen bonds: B:L.277, B:N.280, B:R.283, B:D.315, B:G.319, B:F.351, B:G.352, B:L.355, B:T.379 Water bridges: B:G.317 Salt bridges: B:K.279, B:K.324 Halogen bonds: B:Y.333

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, J. et al., Structural basis for the inhibition of PDK2 by novel ATP- and lipoyl-binding site targeting compounds. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-09-30

Peptides

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial

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