Research workbench
Structure of thr 160 phosphorylated CDK2/CYCLIN a in complex with the inhibitor N-&-N1
Analyse Structure of thr 160 phosphorylated CDK2/CYCLIN a in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DOG
- Type
- protein
- Length
- 1,092 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P30274
- Ligands
- NNN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 298 | 33% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 262 | 67% helix, 0% strand | P30274 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 268 | 35% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 264 | 65% helix, 0% strand | P30274 |
Ligands and binding sites
- NNN · (2R)-2-{[4-(benzylamino)-8-(1-methylethyl)pyrazolo[1,5-a][1,3,5]triazin-2-yl]amino}butan-1-ol · ligand · 2 copies · chains A, C
- SGM · Monothioglycerol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.80 | 0.99 | 24 | empty |
| 2 | 113 | 0.80 | 0.99 | 23 | empty |
| 3 | 967 | 0.78 | 0.80 | 92 | empty |
| 4 | 243 | 0.68 | 0.84 | 27 | NNN |
| 5 | 217 | 0.67 | 0.85 | 26 | NNN |
Interfaces
5 interfaces between chains.
- C–D · 1956 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1905 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 566 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 120 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 3DOG · Structure of Thr 160 phosphorylated CDK2/cyclin A in complex with the inhibitor N-&-N1 · 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 0.91
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 P30274
- Elsewhere: RCSB PDB 3DOG · PDBe 3DOG · UniProt P24941 · UniProt P30274
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