Research workbench
Crystal structure of the kinase domain of human PAK1 in complex with compound 15
Analyse Crystal structure of the kinase domain of human PAK1 in complex with compound 15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P90
- Type
- protein
- Length
- 534 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
- 2K0
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 272 | 46% helix, 15% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 262 | 41% helix, 17% strand | Q13153 |
Ligands and binding sites
- 2K0 · [2-chloro-5-(hydroxymethyl)phenyl]{5-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-1H-pyrrolo[2,3-b]pyridin-3-yl}methanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.65 | 0.79 | 42 | 2K0 |
| 2 | 370 | 0.62 | 0.77 | 37 | 2K0 |
| 3 | 128 | 0.53 | 0.82 | 20 | empty |
| 4 | 78 | 0.35 | 0.76 | 12 | empty |
| 5 | 50 | 0.26 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 303 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4P90 · Crystal structure of the kinase domain of human PAK1 in complex with compound 15 · 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 0.99
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 4P90 · PDBe 4P90 · UniProt Q13153
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