SMTL ID : 6lio.1

Crystal structure of human PDK2 complexed with GM67520

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: L.56, F.64, S.74, F.77, L.78, L.193, Q.196, H.197, I.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74 GOL.6: 5 residues within 4Å: Chain B: R.182, L.396, P.397, V.398, N.400 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.182, B:R.182, B:V.398, B:N.400, B:N.400 GOL.7: 6 residues within 4Å: Chain B: F.61, F.64, S.74, F.77, L.78, Q.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.74 Water bridges: B:H.197

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

SO4.2: 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 SO4.3: 2 residues within 4Å: Chain A: K.258, Q.259 No protein-ligand interaction detected (PLIP) SO4.4: 2 residues within 4Å: Chain A: R.191, N.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.195 Water bridges: A:Y.361 Salt bridges: A:R.191 SO4.8: 5 residues within 4Å: Chain B: R.191, N.195, S.268, H.272, Y.361 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.195, B:S.268, B:Y.361 Salt bridges: B:R.191, B:H.272

2 x EH3: 4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid(Non-covalent)

EH3.5: 22 residues within 4Å: Chain A: E.276, L.277, N.280, A.281, R.283, A.284, D.315, G.317, G.319, V.320, K.324, R.327, L.328, S.330, Y.333, G.352, Y.353, G.354, L.355, P.356, L.371, T.379 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.284, A:V.320, A:K.324, A:L.328, A:T.379 Hydrogen bonds: A:R.283, A:G.319, A:G.319, A:Y.333, A:Y.333, A:G.352, A:G.354, A:L.355, A:T.379 Water bridges: A:D.315, A:G.317, A:F.351, A:Y.353 Salt bridges: A:K.324, A:R.327 EH3.9: 24 residues within 4Å: Chain B: L.277, N.280, A.281, R.283, A.284, D.315, G.317, G.319, V.320, K.324, R.327, L.328, S.330, Y.333, T.335, G.350, F.351, G.352, Y.353, G.354, L.355, P.356, L.371, T.379 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.284, B:V.320, B:L.328, B:T.335, B:T.379 Hydrogen bonds: B:N.280, B:G.319, B:G.319, B:F.351, B:G.352, B:G.354, B:L.355, B:T.379 Water bridges: B:D.315, B:G.317, B:Y.353 Salt bridges: B:K.324, B:R.327

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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