MolNFT v1 · #86638 · protein
Structure of CDK2 in complex with cyclin a and a 2-amino-4- heteroaryl-pyrimidine inhibitor
4BCN · Cyclin-dependent kinase 2: “Structure of CDK2 in complex with cyclin a and a 2-amino-4- heteroaryl-pyrimidine inhibitor”. X-ray diffraction, 2 ligands (T9N, SO4), 14 pockets (best druggability 0.81). MolNFT v1 #86638 on GenesisL1…
- PDB
- 4BCN
- Type
- protein
- Length
- 1,105 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
- T9N, SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 33% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 69% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 296 | 34% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 67% helix, 0% strand | P20248 |
Ligands and binding sites
- T9N · 2-[(3-hydroxyphenyl)amino]-4-[4-methyl-2-(methylamino)-1,3-thiazol-5-yl]pyrimidine-5-carbonitrile · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 2 copies · chains B, C, D
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 | 125 | 0.81 | 0.98 | 24 | empty |
| 2 | 119 | 0.80 | 0.98 | 23 | empty |
| 3 | 1086 | 0.76 | 0.78 | 78 | empty |
| 4 | 442 | 0.69 | 0.80 | 65 | T9N |
| 5 | 358 | 0.67 | 0.81 | 40 | T9N |
Interfaces
5 interfaces between chains.
- C–D · 1651 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1575 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 499 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 444 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 89 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4BCN · 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
- 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 4BCN · PDBe 4BCN · UniProt P24941 · UniProt P20248
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