Research workbench
Crystal structure of PAK1 in complex with an inhibitor compound G-5555
Analyse Crystal structure of PAK1 in complex with an inhibitor compound G-5555 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DEY
- Type
- protein
- Length
- 576 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
- 59T
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 295 | 43% helix, 19% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 281 | 42% helix, 16% strand | Q13153 |
Ligands and binding sites
- 59T · 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino) pyrido[2,3-d]pyrimidin-7(8H)-one · 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 | 846 | 0.75 | 0.79 | 59 | 59T |
| 2 | 502 | 0.65 | 0.77 | 36 | 59T |
| 3 | 264 | 0.57 | 0.77 | 32 | empty |
| 4 | 62 | 0.46 | 0.83 | 15 | empty |
| 5 | 62 | 0.33 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5DEY · Crystal structure of PAK1 in complex with an inhibitor compound G-5555 · 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 0.97
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 Q13153
- Elsewhere: RCSB PDB 5DEY · PDBe 5DEY · UniProt Q13153
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