SMTL ID : 6lil.1

Crystal structure of human PDK2 complexed with an allosteric inhibitor compound 8c

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x FLC: CITRATE ANION(Non-covalent)

FLC.1: 6 residues within 4Å: Chain A: N.149, V.152, R.187, R.191, H.272, Y.361 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Y.361 Salt bridges: A:R.187, A:R.191, A:R.191, A:H.272 FLC.6: 6 residues within 4Å: Chain B: N.149, V.152, R.187, R.191, H.272, Y.361 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.361 Water bridges: B:R.187, B:Y.361, B:Y.361, B:Y.361 Salt bridges: B:R.187, B:R.191, B:R.191, B:H.272

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: N.280, R.283, V.320, L.328, T.335 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.280, A:R.283, A:T.335 PEG.7: 7 residues within 4Å: Chain B: N.280, R.283, L.328, T.335, G.352, G.354, L.355 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.280, B:R.283, B:T.335, B:T.335, B:G.354, B:L.355 Water bridges: B:E.276, B:G.352 PEG.8: 4 residues within 4Å: Chain B: D.228, P.267, S.268, Y.271 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.228

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.225, D.228, P.267, Y.271 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.228

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

SO4.4: 4 residues within 4Å: Chain A: R.182, L.185, K.363, R.395 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.181, A:D.181 Salt bridges: A:K.363, A:R.395

2 x EGX: 1-(1-piperidin-4-ylpyrazol-4-yl)anthracene-9,10-dione(Non-covalent)

EGX.5: 7 residues within 4Å: Chain A: L.56, Q.60, F.61, F.64, T.73, S.74, F.77 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.56, A:Q.60, A:F.61, A:F.64, A:F.64, A:F.64, A:F.64, A:F.64, A:T.73, A:F.77 Hydrogen bonds: A:Q.60 Water bridges: A:S.54 pi-Stacking: A:F.77 EGX.9: 8 residues within 4Å: Chain B: S.54, L.56, Q.60, F.61, F.64, T.73, S.74, F.77 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.56, B:Q.60, B:F.61, B:F.64, B:F.64, B:F.64, B:F.64, B:T.73, B:F.77 Hydrogen bonds: B:Q.60 pi-Stacking: B:F.64, B:F.77, B:F.77

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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