Research workbench
Cdk-2-cyclin complex with indazole inhibitor 9 bound at its active site
Analyse Cdk-2-cyclin complex with indazole inhibitor 9 bound at its active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F5X
- Type
- protein
- Length
- 1,106 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- EZV, SO4
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 297 | 34% helix, 18% strand | P24941 |
| B | Cyclin-A2 | protein | 256 | 66% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 66% helix, 0% strand | P20248 |
Ligands and binding sites
- EZV · 4-{3-[7-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-indazol-6-yl}aniline · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.79 | 0.96 | 26 | empty |
| 2 | 158 | 0.78 | 0.94 | 27 | empty |
| 3 | 383 | 0.70 | 0.82 | 41 | EZV |
| 4 | 365 | 0.68 | 0.81 | 40 | EZV |
| 5 | 293 | 0.59 | 0.78 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1670 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3F5X · CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P24941
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 3F5X · PDBe 3F5X · UniProt P24941 · UniProt P20248
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