MolNFT v1 · #87936 · protein
Structure-based design of C8-substituted O6- cyclohexylmethoxyguanine CDK1 and 2 inhibitors.
4CFW · Cyclin-dependent kinase 2: “Structure-based design of C8-substituted O6- cyclohexylmethoxyguanine CDK1 and 2 inhibitors.”. X-ray diffraction, 1 ligand (SQ9), 14 pockets (best druggability 0.81). MolNFT v1 #87936 on GenesisL1: 3D…
- PDB
- 4CFW
- Type
- protein
- Length
- 1,113 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
- SQ9
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 51% 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 | 300 | 34% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 69% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22, 2.7.11.23) | protein | 298 | 35% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 257 | 69% helix, 0% strand | P20248 |
Ligands and binding sites
- SQ9 · 3-[2-amino-6-(cyclohexylmethoxy)-7H-purin-8-yl]-2-methylbenzenesulfonamide · ligand · 2 copies · chains A, C
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 | 135 | 0.81 | 0.98 | 25 | empty |
| 2 | 124 | 0.80 | 0.98 | 25 | empty |
| 3 | 805 | 0.78 | 0.82 | 106 | empty |
| 4 | 247 | 0.68 | 0.84 | 26 | SQ9 |
| 5 | 266 | 0.65 | 0.81 | 26 | SQ9 |
Interfaces
5 interfaces between chains.
- A–B · 1680 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1660 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 526 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 470 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 130 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4CFW · 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 4CFW · PDBe 4CFW · UniProt P24941 · UniProt P20248
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