Research workbench
The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 1
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
- 7VDP
- Type
- protein
- Length
- 845 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
- 65L, CL
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent-like kinase 5 (EC 2.7.11.1) | protein | 287 | 34% helix, 17% strand | Q00535 |
| B | Cyclin-dependent-like kinase 5 (EC 2.7.11.1) | protein | 279 | 37% helix, 17% 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 | 131 | 69% helix, 0% strand | Q15078 |
Ligands and binding sites
- 65L · [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 7 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.82 | 0.83 | 106 | 65L, EDO, CL, GOL |
| 2 | 382 | 0.68 | 0.81 | 32 | empty |
| 3 | 105 | 0.59 | 0.86 | 22 | empty |
| 4 | 100 | 0.46 | 0.80 | 21 | CL |
| 5 | 58 | 0.39 | 0.80 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1486 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1420 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7VDP · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 1 · 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 B 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 Q00535
- Every structure of UniProt Q15078
- Elsewhere: RCSB PDB 7VDP · PDBe 7VDP · UniProt Q00535 · UniProt Q15078
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