Research workbench
The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 13
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
- 7VDR
- Type
- protein
- Length
- 849 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
- 63I
- Pockets
- 12 · best druggability 0.75
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 | 34% helix, 18% strand | Q00535 |
| B | Cyclin-dependent-like kinase 5 (EC 2.7.11.1) | protein | 275 | 36% helix, 17% strand | Q00535 |
| C | Cyclin-dependent kinase 5 activator 1, P25 | protein | 148 | 69% helix, 0% strand | Q15078 |
| D | Cyclin-dependent kinase 5 activator 1, P25 | protein | 136 | 68% helix, 0% strand | Q15078 |
Ligands and binding sites
- 63I · (1R)-1-[7-[(2-fluoranyl-4-pyrazol-1-yl-phenyl)amino]-1, 6-naphthyridin-2-yl]-1-(1-methylpiperidin-4-yl)ethanol · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.75 | 0.87 | 30 | 63I, PGE |
| 2 | 308 | 0.72 | 0.85 | 35 | empty |
| 3 | 282 | 0.68 | 0.83 | 40 | empty |
| 4 | 202 | 0.66 | 0.84 | 22 | 63I |
| 5 | 147 | 0.63 | 0.85 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1623 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1424 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 947 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7VDR · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 13 · 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 7VDR · PDBe 7VDR · UniProt Q00535 · UniProt Q15078
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