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Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 7
Analyse Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VBV
- Type
- protein
- Length
- 673 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q15119
- Ligands
- 67V, CL
- Pockets
- 11 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 337 | 56% helix, 15% strand | Q15119 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 336 | 56% helix, 15% strand | Q15119 |
Ligands and binding sites
- 67V · methyl 8-cyclopropyl-2-methyl-9H-pyrido[2,3-b]indole-3-carboxylate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.69 | 0.97 | 14 | DMS |
| 2 | 164 | 0.67 | 0.86 | 24 | DMS |
| 3 | 174 | 0.66 | 0.86 | 28 | 67V |
| 4 | 314 | 0.63 | 0.79 | 34 | empty |
| 5 | 99 | 0.62 | 0.88 | 21 | DMS |
Interfaces
1 interface between chains.
- A–B · 1236 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7VBV · Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 7 · the same entry in another collection · chain A against A, TM-score 1.00
- Q15119 · AlphaFold monomer V2.0 prediction for [pyruvate dehydrogenase (acetyl-transferring)]… · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q15119
- Elsewhere: RCSB PDB 7VBV · PDBe 7VBV · UniProt Q15119
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