SMTL ID : 7vbv.1

Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 7

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 3 residues within 4Å: Chain A: R.149, I.150, Y.323 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.150 Hydrogen bonds: A:Y.323 Salt bridges: A:R.149 ACT.2: 6 residues within 4Å: Chain A: Y.75, H.110, R.149, I.152, R.153, I.156 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.3: 4 residues within 4Å: Chain A: D.143, L.147, L.322, R.357 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:D.143, A:L.147, A:L.322 Salt bridges: A:K.325, A:R.357 ACT.8: 5 residues within 4Å: Chain B: V.114, Y.146, R.149, I.150, Y.323 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.146 Salt bridges: B:R.149 ACT.9: 7 residues within 4Å: Chain B: I.106, R.107, H.110, R.149, I.152, R.153 Ligands: CL.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.149, 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, S.36, F.39, L.40, L.155, Q.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.36 Water bridges: A:Q.158 pi-Cation interactions: A:F.26 DMS.5: 5 residues within 4Å: Chain A: V.62, G.120, V.121, Y.124, I.138 No protein-ligand interaction detected (PLIP) DMS.10: 4 residues within 4Å: Chain B: S.36, Q.158, H.159, F.163 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain B: S.67, V.68, M.117, G.120, V.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.67

2 x 67V: methyl 8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole-3-carboxylate(Non-covalent)

67V.6: 15 residues within 4Å: Chain A: L.239, N.242, A.243, A.246, M.275, D.277, G.279, G.281, V.282, L.290, L.317, L.333, T.341, D.342, A.343 11 PLIP interactions: 11 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.333, A:A.343 Hydrogen bonds: A:D.277 Water bridges: A:G.281, A:T.341 67V.12: 16 residues within 4Å: Chain B: L.239, N.242, A.243, A.246, M.275, D.277, G.279, G.281, V.282, K.286, L.290, F.313, L.333, T.341, D.342, A.343 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.239, B:N.242, B:A.243, B:F.313, B:L.333, B:T.341, B:A.343 Hydrogen bonds: B:D.277 Water bridges: B:G.281, B:T.341 Salt bridges: B:K.286

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

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

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
B

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

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