Research workbench
Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2
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
- 7EAS
- Type
- protein
- Length
- 341 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Homo sapiens
- Molecule
- [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q15119
- Ligands
- 42A, CL
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · resolution 1.97 · 1 distinct chain · 57% 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 | 341 | 57% helix, 15% strand | Q15119 |
Ligands and binding sites
- 42A · 1H-pyrrolo[2,3-b]pyridine-3-carbonitrile · ligand · chains A
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.61 | 0.87 | 19 | DMS |
| 2 | 160 | 0.53 | 0.79 | 26 | 42A |
| 3 | 126 | 0.42 | 0.76 | 20 | ACT |
Compared structures
- 7EAS · Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 2 · 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 7EAS · PDBe 7EAS · UniProt Q15119
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