Research workbench
Crystal structure of P21 activated kinase 1 in complex with an inhibitor compound 4
Analyse Crystal structure of P21 activated kinase 1 in complex with an inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZY4
- Type
- protein
- Length
- 580 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
- 4T3, SO4
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 288 | 41% helix, 16% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 292 | 42% helix, 16% strand | Q13153 |
Ligands and binding sites
- 4T3 · 2-(4-aminopiperidin-1-yl)-N-(5-cyclopropyl-1H-pyrazol-3-yl)thieno[3,2-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains 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 | 791 | 0.78 | 0.81 | 81 | 4T3, DMS |
| 2 | 697 | 0.75 | 0.81 | 50 | 4T3 |
| 3 | 186 | 0.50 | 0.77 | 23 | SO4 |
| 4 | 65 | 0.48 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4ZY4 · Crystal structure of P21 activated kinase 1 in complex with an inhibitor compound 4 · 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 4ZY4 · PDBe 4ZY4 · UniProt Q13153
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