Research workbench
The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 7
Analyse The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VDQ
- Type
- protein
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent-like kinase 5; Cyclin-dependent kinase 5 activator 1, P25
- EC
- 2.7.11.1
- UniProt
- Q00535, Q15078
- Ligands
- 64V
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent-like kinase 5 (EC 2.7.11.1) | protein | 290 | 35% helix, 18% strand | Q00535 |
| B | Cyclin-dependent-like kinase 5 (EC 2.7.11.1) | protein | 277 | 36% helix, 16% strand | Q00535 |
| C | Cyclin-dependent kinase 5 activator 1, P25 | protein | 148 | 70% helix, 0% strand | Q15078 |
| D | Cyclin-dependent kinase 5 activator 1, P25 | protein | 136 | 66% helix, 0% strand | Q15078 |
Ligands and binding sites
- 64V · 2-[[7-[[2-fluoranyl-4-[3-(hydroxymethyl)pyrazol-1-yl]phenyl]amino]-1,6-naphthyridin-2-yl]-(1-methylpiperidin-4-yl)amino]ethanoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.77 | 0.82 | 59 | 64V |
| 2 | 486 | 0.75 | 0.83 | 43 | 64V |
| 3 | 53 | 0.72 | 0.98 | 17 | empty |
| 4 | 300 | 0.68 | 0.82 | 38 | empty |
| 5 | 197 | 0.60 | 0.82 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1594 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1509 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 972 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7VDQ · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 7 · the same entry in another collection · chain D against D, TM-score 1.00
- Q15078 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 5 activator 1 (Q15078) · a predicted model of the same protein · chain C against A, TM-score 1.00
- Q00535 · AlphaFold monomer V2.0 prediction for cyclin-dependent-like kinase 5 (Q00535) · 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 Q00535
- Every structure of UniProt Q15078
- Elsewhere: RCSB PDB 7VDQ · PDBe 7VDQ · UniProt Q00535 · UniProt Q15078
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.