Research workbench
CDK2/CYCLINA in complex with SU9516
Analyse CDK2/CYCLINA in complex with SU9516 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GUC
- Type
- protein
- Length
- 1,111 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, P30274
- Ligands
- SU9
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 292 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 261 | 67% helix, 0% strand | P30274 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 34% helix, 18% strand | P24941 |
Ligands and binding sites
- SU9 · (3Z)-3-(1H-imidazol-5-ylmethylene)-5-methoxy-1H-indol-2(3H)-one · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.82 | 0.98 | 23 | empty |
| 2 | 137 | 0.81 | 0.98 | 24 | empty |
| 3 | 651 | 0.78 | 0.83 | 72 | empty |
| 4 | 208 | 0.67 | 0.85 | 26 | SU9 |
| 5 | 268 | 0.67 | 0.82 | 33 | SU9 |
Interfaces
5 interfaces between chains.
- C–D · 1934 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1897 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 550 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 504 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6GUC · CDK2/CyclinA in complex with SU9516 · the same entry in another collection · chain D against D, TM-score 1.00
- P30274 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P30274) · 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 0.92
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 P30274
- Elsewhere: RCSB PDB 6GUC · PDBe 6GUC · UniProt P24941 · UniProt P30274
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