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… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CFV
- Type
- protein
- Length
- 1,090 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
- 75X, MG
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22, 2.7.11.23) | protein | 301 | 36% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 262 | 68% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22, 2.7.11.23) | protein | 265 | 38% helix, 19% strand | P24941 |
Ligands and binding sites
- 75X · 3-[2-amino-6-(cyclohexylmethoxy)-7H-purin-8-yl]-2-methylphenol · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.81 | 0.99 | 23 | MG |
| 2 | 120 | 0.80 | 0.98 | 22 | MG |
| 3 | 733 | 0.74 | 0.79 | 75 | empty |
| 4 | 330 | 0.67 | 0.81 | 33 | 75X |
| 5 | 277 | 0.66 | 0.82 | 35 | 75X |
Interfaces
5 interfaces between chains.
- C–D · 1933 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1859 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 551 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 471 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4CFV · Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2… · the same entry in another collection · chain C against C, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 0.90
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 4CFV · PDBe 4CFV · UniProt P24941 · UniProt P20248
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