Research workbench
The synthesis and evaluation of diazaspirocyclic protein kinase inhibitors
Analyse The synthesis and evaluation of diazaspirocyclic protein kinase inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZO2
- Type
- protein
- Length
- 362 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
- EC
- 2.7.11.11
- UniProt
- P00517, P63248
- Ligands
- 15I
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11) | protein | 344 | 37% helix, 15% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 18 | 39% helix, 0% strand | P63248 |
Ligands and binding sites
- 15I · 6-(2,9-Diazaspiro[5.5]undecan-9-yl)-9H-purine · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.77 | 0.87 | 43 | 15I |
| 2 | 241 | 0.54 | 0.77 | 37 | GOL |
| 3 | 91 | 0.40 | 0.77 | 19 | empty |
| 4 | 81 | 0.33 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–I · 859 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 3ZO2 · The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- P63248 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain I against A, TM-score 0.44
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 P00517
- Every structure of UniProt P63248
- Elsewhere: RCSB PDB 3ZO2 · PDBe 3ZO2 · UniProt P00517 · UniProt P63248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.