SMTL ID : 7eas.1

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: Y.75, H.110, V.113, R.149 Ligands: ACT.3 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: Y.75, H.110, V.113, R.149 Ligands: ACT.9 Ligand excluded by PLIP

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: Y.146, R.149, I.150, I.319, Y.323 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.146, A:I.150, A:I.319 Hydrogen bonds: A:Y.323 Salt bridges: A:R.149 ACT.3: 8 residues within 4Å: Chain A: I.106, R.107, H.110, R.149, I.152, R.153, I.156 Ligands: CL.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.106, A:R.153, A:I.156 Salt bridges: A:H.110, A:R.149, A:R.153 ACT.8: 5 residues within 4Å: Chain B: Y.146, R.149, I.150, I.319, Y.323 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.146, B:I.150, B:I.319 Hydrogen bonds: B:Y.323 Salt bridges: B:R.149 ACT.9: 8 residues within 4Å: Chain B: I.106, R.107, H.110, R.149, I.152, R.153, I.156 Ligands: CL.7 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.106, B:R.153, B:I.156 Salt bridges: B:H.110, B:R.149, B:R.153

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 6 residues within 4Å: Chain A: F.23, F.26, S.36, F.39, L.40, Q.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.36 Water bridges: A:G.27 DMS.5: 5 residues within 4Å: Chain A: S.67, V.68, M.117, G.120, F.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.67 DMS.10: 6 residues within 4Å: Chain B: F.23, F.26, S.36, F.39, L.40, Q.158 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.36 Water bridges: B:G.27 DMS.11: 5 residues within 4Å: Chain B: S.67, V.68, M.117, G.120, F.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.67

2 x 42A: 1H-pyrrolo[2,3-b]pyridine-3-carbonitrile(Non-covalent)

42A.6: 9 residues within 4Å: Chain A: L.239, N.242, A.243, A.246, D.277, V.282, L.317, L.333, T.341 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.242, A:V.282 Hydrogen bonds: A:N.242, A:D.277 Water bridges: A:T.341, A:T.341 42A.12: 9 residues within 4Å: Chain B: L.239, N.242, A.243, A.246, D.277, V.282, L.317, L.333, T.341 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:N.242, B:V.282 Hydrogen bonds: B:N.242, B:D.277 Water bridges: B:T.341, B:T.341

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 2, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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