SMTL ID : 7vbu.1

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 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.8: 5 residues within 4Å: Chain B: Y.75, H.110, V.113, R.149 Ligands: ACT.10 Ligand excluded by PLIP

6 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.4: 3 residues within 4Å: Chain A: R.144, L.147, R.357 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:R.144, A:L.147 Water bridges: A:K.325, A:R.357, A:R.357 Salt bridges: A:K.325, A:R.357 ACT.9: 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.10: 7 residues within 4Å: Chain B: Y.75, H.110, R.149, I.152, R.153, I.156 Ligands: CL.8 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.152 Salt bridges: B:H.110, B:R.149, B:R.153 ACT.11: 3 residues within 4Å: Chain B: R.144, L.147, R.357 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.144, B:L.147 Water bridges: B:K.325, B:R.357, B:R.357 Salt bridges: B:K.325, B:R.357

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

DMS.5: 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.6: 3 residues within 4Å: Chain A: V.62, V.68, F.141 No protein-ligand interaction detected (PLIP) DMS.12: 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.13: 3 residues within 4Å: Chain B: V.62, V.68, F.141 No protein-ligand interaction detected (PLIP)

2 x 6I4: 8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole(Non-covalent)

6I4.7: 14 residues within 4Å: Chain A: L.239, N.242, A.243, A.246, M.275, D.277, G.279, G.281, V.282, L.317, L.333, T.341, D.342, A.343 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.239, A:N.242, A:A.243, A:A.246, A:V.282, A:L.317, A:L.317, A:L.333, A:T.341, A:A.343 Hydrogen bonds: A:D.277 Water bridges: A:T.341, A:T.341 6I4.14: 14 residues within 4Å: Chain B: L.239, N.242, A.243, A.246, M.275, D.277, G.279, G.281, V.282, L.317, L.333, T.341, D.342, A.343 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.239, B:N.242, B:A.243, B:A.246, B:V.282, B:L.317, B:L.317, B:L.333, 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

Bessho, Y. et al., Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors. Bioorg.Med.Chem. (2021)

Release Date

2022-02-16

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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