MolNFT v1 · #189388 · protein
The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 24
7VDS · Cyclin-dependent-like kinase 5, P25: “The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 24”. X-ray diffraction, 2 ligands (61U, CL), 14 pockets (best druggability 0.70). MolNFT v1 #189388 on…
- PDB
- 7VDS
- Type
- protein
- Length
- 863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent-like kinase 5, P25; Cyclin-dependent kinase 5 activator 1
- EC
- 2.7.11.1
- UniProt
- Q00535, Q15078
- Ligands
- 61U, CL
- Pockets
- 14 · best druggability 0.70
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, P25 (EC 2.7.11.1) | protein | 290 | 34% helix, 18% strand | Q00535 |
| B | Cyclin-dependent-like kinase 5, P25 (EC 2.7.11.1) | protein | 278 | 36% helix, 16% strand | Q00535 |
| C | Cyclin-dependent kinase 5 activator 1 | protein | 148 | 67% helix, 0% strand | Q15078 |
| D | Cyclin-dependent kinase 5 activator 1 | protein | 147 | 68% helix, 0% strand | Q15078 |
Ligands and binding sites
- 61U · 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile · ligand · chains A
- CL · Chloride ion · ion · 19 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C
- GOL · Glycerol · additive · 8 copies · chains A, C
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 | 385 | 0.70 | 0.81 | 36 | 61U, CL |
| 2 | 98 | 0.68 | 0.92 | 19 | empty |
| 3 | 460 | 0.66 | 0.78 | 40 | empty |
| 4 | 172 | 0.57 | 0.81 | 27 | GOL |
| 5 | 81 | 0.54 | 0.85 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1506 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 1397 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1224 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 7VDS · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 · 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 7VDS · PDBe 7VDS · UniProt Q00535 · UniProt Q15078
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