Research workbench
Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA1
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
- 4MP2
- Type
- protein
- Length
- 360 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
- PV1
- Pockets
- 4 · best druggability 0.57
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 | 360 | 53% helix, 14% strand | Q15119 |
Ligands and binding sites
- PV1 · (5-bromo-2,4-dihydroxyphenyl)(1,3-dihydro-2H-isoindol-2-yl)methanone · 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.57 | 0.89 | 14 | empty |
| 2 | 143 | 0.51 | 0.79 | 29 | PV1 |
| 3 | 144 | 0.43 | 0.75 | 21 | empty |
| 4 | 53 | 0.29 | 0.75 | 9 | empty |
Compared structures
- 4MP2 · Crystal structure of pyruvate dehydrogenase kinase isoform 2 in complex with inhibitor PA1 · 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 4MP2 · PDBe 4MP2 · UniProt Q15119
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