Research workbench
Structural mechanism for the inhibition of CDK5-P25 by roscovitine, aloisine and indirubin.
Analyse Structural mechanism for the inhibition of CDK5-P25 by roscovitine, aloisine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UNH
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 5; Cyclin-dependent kinase 5 activator 1
- EC
- 2.7.11.22
- UniProt
- Q00535, Q15078
- Ligands
- IXM
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cyclin-dependent kinase 5 (EC 2.7.11.22) | protein | 276 | 37% helix, 16% strand | Q00535 |
| D, E | Cyclin-dependent kinase 5 activator 1 | protein | 147 | 69% helix, 0% strand | Q15078 |
Ligands and binding sites
- IXM · (Z)-1H,1'H-[2,3']biindolylidene-3,2'-dione-3-oxime · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.76 | 0.78 | 133 | IXM |
| 2 | 113 | 0.43 | 0.77 | 22 | empty |
| 3 | 73 | 0.33 | 0.75 | 18 | empty |
| 4 | 57 | 0.32 | 0.77 | 16 | empty |
| 5 | 61 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1479 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 1450 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 821 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1UNH · Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and… · 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 E against A, TM-score 0.98
- 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 1UNH · PDBe 1UNH · UniProt Q00535 · UniProt Q15078
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