Research workbench
CDK2/CYCLIN a covalent complex with 6-(cyclohexylmethoxy)-N-(4- (VINYLSULFONYL)PHENYL)-9H-purin-2-amine (NU6300)
Analyse CDK2/CYCLIN a covalent complex with 6-(cyclohexylmethoxy)-N-(4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CYI
- Type
- protein
- Length
- 1,110 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
- UniProt
- P24941, P20248
- Ligands
- 55S
- Pockets
- 14 · best druggability 0.80
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) | protein | 299 | 34% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 69% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 35% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 256 | 69% helix, 0% strand | P20248 |
Ligands and binding sites
- 55S · 6-(cyclohexylmethoxy)-N-[4-(ethylsulfonyl)phenyl]-9H-purin-2-amine · 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.80 | 0.98 | 23 | empty |
| 2 | 124 | 0.80 | 0.98 | 24 | empty |
| 3 | 1077 | 0.77 | 0.79 | 85 | empty |
| 4 | 223 | 0.68 | 0.85 | 28 | 55S |
| 5 | 249 | 0.67 | 0.84 | 27 | 55S |
Interfaces
5 interfaces between chains.
- A–B · 1690 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1611 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 484 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 114 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, phosphorylation).
Compared structures
- 5CYI · CDK2/Cyclin A covalent complex with 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-p… · 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 B 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 5CYI · PDBe 5CYI · UniProt P24941 · UniProt P20248
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