MolNFT v1 · #32992 · protein
Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor
2C6T · Cell division protein kinase 2: “Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor”. X-ray diffraction, 1 ligand (DT5), 10 pockets (best druggability 0.79). MolNFT v1 #32992 on GenesisL1: 3D…
- PDB
- 2C6T
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- DT5
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
Ligands and binding sites
- DT5 · 4-{[5-(cyclohexyloxy)[1,2,4]triazolo[1,5-a]pyrimidin-7-yl]amino}benzenesulfonamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.79 | 0.81 | 70 | empty |
| 2 | 145 | 0.78 | 0.95 | 23 | empty |
| 3 | 151 | 0.78 | 0.95 | 26 | empty |
| 4 | 1044 | 0.77 | 0.79 | 80 | empty |
| 5 | 902 | 0.77 | 0.80 | 93 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1721 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1681 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 442 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 351 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 310 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 2C6T · Crystal structure of the human CDK2 complexed with the triazolopyrimidine inhibitor · 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 D 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 0.91
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 P20248
- Elsewhere: RCSB PDB 2C6T · PDBe 2C6T · UniProt P24941 · UniProt P20248
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