Research workbench
Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2 inhibitors.
Analyse Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CFN
- Type
- protein
- Length
- 1,103 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P24941, P20248
- Ligands
- JYM
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22, 2.7.11.23) | protein | 297 | 35% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 254 | 68% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22, 2.7.11.23) | protein | 297 | 35% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 67% helix, 0% strand | P20248 |
Ligands and binding sites
- JYM · 6-(cyclohexylmethoxy)-8-(trifluoromethyl)-9H-purin-2-amine · ligand · 2 copies · chains A, C
- DTT · 2,3-dihydroxy-1,4-dithiobutane · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.81 | 0.98 | 25 | empty |
| 2 | 117 | 0.80 | 0.99 | 22 | empty |
| 3 | 210 | 0.71 | 0.87 | 27 | JYM |
| 4 | 244 | 0.64 | 0.82 | 28 | JYM |
| 5 | 252 | 0.59 | 0.80 | 35 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1700 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1622 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 75 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4CFN · Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2… · 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 C against A, TM-score 0.91
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 4CFN · PDBe 4CFN · UniProt P24941 · UniProt P20248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.