MolNFT v1 · #112860 · protein
Crystal structure of P21-activated kinase 1 in complex with an inhibitor compound 17
4ZY5 · SERINE/THREONINE-protein kinase pak 1: “Crystal structure of P21-activated kinase 1 in complex with an inhibitor compound 17”. X-ray diffraction, 2 ligands (4T5, SO4), 5 pockets (best druggability 0.77). MolNFT v1 #112860 on…
- PDB
- 4ZY5
- Type
- protein
- Length
- 570 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
- 4T5, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 283 | 42% helix, 13% strand | Q13153 |
| B | SERINE/THREONINE-protein kinase pak 1 (EC 2.7.11.1) | protein | 287 | 41% helix, 15% strand | Q13153 |
Ligands and binding sites
- 4T5 · N~2~-[(trans-4-aminocyclohexyl)methyl]-N~4~-(3-cyclopropyl-1H-pyrazol-5-yl)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · 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
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 | 767 | 0.77 | 0.81 | 68 | 4T5, SO4 |
| 2 | 647 | 0.72 | 0.79 | 53 | 4T5, DMS |
| 3 | 302 | 0.70 | 0.84 | 40 | empty |
| 4 | 61 | 0.37 | 0.78 | 14 | empty |
| 5 | 80 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4ZY5 · Crystal Structure of p21-activated kinase 1 in complex with an inhibitor compound 17 · 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 4ZY5 · PDBe 4ZY5 · UniProt Q13153
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