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
- 3ZO4
- Type
- protein
- Length
- 357 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, Q3SX13
- Ligands
- QWI
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 36% 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 | 337 | 36% helix, 15% strand | P00517 |
| I | Camp-dependent protein kinase inhibitor alpha | protein | 20 | 30% helix, 0% strand | Q3SX13 |
Ligands and binding sites
- QWI · 6-(4-phenyl-1,9-diazaspiro[5.5]undecan-9-yl)-9H-purine · ligand · chains A, I
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.81 | 0.91 | 41 | QWI |
| 2 | 85 | 0.45 | 0.79 | 12 | GOL |
| 3 | 78 | 0.32 | 0.74 | 23 | empty |
| 4 | 58 | 0.32 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–I · 1042 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 3ZO4 · The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors · the same entry in another collection · chain A against A, TM-score 1.00
- Q3SX13 · 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 0.41
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 Q3SX13
- Elsewhere: RCSB PDB 3ZO4 · PDBe 3ZO4 · UniProt P00517 · UniProt Q3SX13
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