SMTL ID : 7ebh.1

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 13

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 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: 7 residues within 4Å: Chain A: Y.75, H.110, R.149, I.152, R.153, I.156 Ligands: CL.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.152 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: 7 residues within 4Å: Chain B: Y.75, H.110, R.149, I.152, R.153, I.156 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.152 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 No protein-ligand interaction detected (PLIP) DMS.5: 5 residues within 4Å: Chain A: V.62, V.68, G.120, V.121, F.141 No protein-ligand interaction detected (PLIP) DMS.10: 6 residues within 4Å: Chain B: F.23, F.26, S.36, F.39, L.40, Q.158 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain B: V.62, V.68, G.120, V.121, F.141 No protein-ligand interaction detected (PLIP)

2 x J0F: 5-bromanyl-2-methyl-6-propyl-7H-pyrrolo[2,3-d]pyrimidine(Non-covalent)

J0F.6: 12 residues within 4Å: Chain A: L.239, N.242, A.243, A.246, M.275, D.277, G.281, V.282, L.317, L.333, T.341, A.343 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.246, A:M.275, A:V.282, A:T.341, A:A.343 Hydrogen bonds: A:D.277 Water bridges: A:T.341, A:T.341 J0F.12: 12 residues within 4Å: Chain B: L.239, N.242, A.243, A.246, M.275, D.277, G.281, V.282, L.317, L.333, T.341, A.343 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.246, B:M.275, B:V.282, B:T.341, B:A.343 Hydrogen bonds: 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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