Research workbench
The structure of cyclin dependent kinase 2 (CKD2) with a pyrazolobenzodiazepine inhibitor
Analyse The structure of cyclin dependent kinase 2 (CKD2) with a pyrazolobenzodiazepine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LE6
- Type
- protein
- Length
- 283 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2
- EC
- 2.7.11.22
- UniProt
- P24941
- Ligands
- 2BZ
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 283 | 36% helix, 16% strand | P24941 |
Ligands and binding sites
- 2BZ · 5-(2-chlorophenyl)-3-methyl-7-nitropyrazolo[3,4-b][1,4]benzodiazepine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.68 | 0.84 | 27 | 2BZ |
| 2 | 50 | 0.64 | 0.94 | 18 | empty |
| 3 | 57 | 0.34 | 0.78 | 14 | empty |
Compared structures
- 3LE6 · The structure of cyclin dependent kinase 2 (CKD2) with a pyrazolobenzodiazepine inhibitor · the same entry in another collection · chain A 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 0.95
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
- Elsewhere: RCSB PDB 3LE6 · PDBe 3LE6 · UniProt P24941
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