Research workbench
Back pocket flexibility provides group-II pak selectivity for type 1 kinase inhibitors
Analyse Back pocket flexibility provides group-II pak selectivity for type 1 kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O0T
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pak 1
- EC
- 2.7.11.1
- UniProt
- Q13153
- Ligands
- 2OL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 292 | 38% helix, 19% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 280 | 42% helix, 17% strand | Q13153 |
Ligands and binding sites
- 2OL · 1-({1-(2-aminopyrimidin-4-yl)-2-[(2-methoxyethyl)amino]-1H-benzimidazol-6-yl}ethynyl)cyclohexanol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.69 | 0.81 | 39 | 2OL |
| 2 | 503 | 0.68 | 0.79 | 52 | empty |
| 3 | 247 | 0.55 | 0.77 | 31 | empty |
| 4 | 237 | 0.53 | 0.76 | 35 | empty |
| 5 | 51 | 0.42 | 0.83 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 892 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4O0T · Back pocket flexibility provides group-II PAK selectivity for type 1 kinase inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q13153 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pak 1 (Q13153) · 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 Q13153
- Elsewhere: RCSB PDB 4O0T · PDBe 4O0T · UniProt Q13153
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