Research workbench
PDK1 in complex with inhibitor MP6
Analyse PDK1 in complex with inhibitor MP6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NAY
- Type
- protein
- Length
- 558 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoinositide-dependent protein kinase 1
- EC
- 2.7.11.1
- UniProt
- O15530
- Ligands
- MP6
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-phosphoinositide-dependent protein kinase 1 (EC 2.7.11.1) | protein | 279 | 39% helix, 18% strand | O15530 |
Ligands and binding sites
- MP6 · 4-(2-cyclopropylethylidene)-9-(1H-pyrazol-4-yl)-6-{[(1R)-1,2,2-trimethylpropyl]amino}benzo[c][1,6]naphthyridin-1(4H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.70 | 0.82 | 42 | MP6 |
| 2 | 363 | 0.69 | 0.82 | 43 | MP6 |
| 3 | 432 | 0.63 | 0.77 | 30 | empty |
| 4 | 52 | 0.27 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3NAY · PDK1 in complex with inhibitor MP6 · the same entry in another collection · chain A against A, TM-score 1.00
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 O15530
- Elsewhere: RCSB PDB 3NAY · PDBe 3NAY · UniProt O15530
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