Research workbench
Structure of CDK2 in complex with cyclin a and a 2-amino-4- heteroaryl-pyrimidine inhibitor
Analyse Structure of CDK2 in complex with cyclin a and a 2-amino-4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BCQ
- Type
- protein
- Length
- 1,097 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
- TJF
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 293 | 34% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 66% helix, 0% strand | P30274 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 293 | 34% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 254 | 65% helix, 0% strand | P30274 |
Ligands and binding sites
- TJF · 4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]-2-{[3-(morpholin-4-ylcarbonyl)phenyl]amino}pyrimidine-5-carbonitrile · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.96 | 25 | empty |
| 2 | 176 | 0.81 | 0.96 | 25 | empty |
| 3 | 655 | 0.71 | 0.78 | 60 | empty |
| 4 | 337 | 0.68 | 0.82 | 28 | TJF |
| 5 | 387 | 0.67 | 0.80 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1623 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1620 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 506 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 430 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4BCQ · Structure of CDK2 in complex with cyclin A and a 2-amino-4-heteroaryl- pyrimidine… · 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 0.98
- 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 0.90
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 P30274
- Elsewhere: RCSB PDB 4BCQ · PDBe 4BCQ · UniProt P24941 · UniProt P30274
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