Research workbench
Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PS10
Analyse Crystal structure of pyruvate dehydrogenase kinase isoform 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
- 4MPN
- Type
- protein
- Length
- 363 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial
- EC
- 2.7.11.2
- UniProt
- Q15119
- Ligands
- PV0
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 363 | 53% helix, 14% strand | Q15119 |
Ligands and binding sites
- PV0 · 2-[(2,4-dihydroxyphenyl)sulfonyl]-2,3-dihydro-1H-isoindole-4,6-diol · ligand · chains A
- TLA · L(+)-tartaric acid · additive · 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 | 75 | 0.58 | 0.87 | 13 | empty |
| 2 | 221 | 0.54 | 0.78 | 30 | PV0 |
| 3 | 120 | 0.42 | 0.76 | 21 | empty |
Compared structures
- 4MPN · Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor… · 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 0.98
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 4MPN · PDBe 4MPN · UniProt Q15119
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