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Crystal structure of human PDK2 complexed with GM67520
Analyse Crystal structure of human PDK2 complexed with GM67520 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LIO
- Type
- protein
- Length
- 725 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
- EH3, SO4
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 354 | 54% helix, 14% strand | Q15119 |
| B | [pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial (EC 2.7.11.2) | protein | 371 | 51% helix, 14% strand | Q15119 |
Ligands and binding sites
- EH3 · 4-[[[5-[5-chloranyl-2,4-bis(oxidanyl)phenyl]-4-[4-(1-methylsulfonylpiperidin-4-yl)oxyphenyl]-1,2-oxazol-3-yl]carbonylamino]methyl]cyclohexane-1-carboxylic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.70 | 0.84 | 38 | EH3 |
| 2 | 387 | 0.65 | 0.79 | 37 | empty |
| 3 | 56 | 0.65 | 0.94 | 13 | GOL |
| 4 | 449 | 0.65 | 0.78 | 52 | EH3 |
| 5 | 252 | 0.54 | 0.76 | 30 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1240 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6LIO · Crystal structure of human PDK2 complexed with GM67520 · 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 6LIO · PDBe 6LIO · UniProt Q15119
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