MolNFT v1 · #189390 · protein
The structure of cyclin-dependent kinase 2 (CDK2) in complex with compound 1
7VDU: “The structure of cyclin-dependent kinase 2 (CDK2) in complex with compound 1”. X-ray diffraction, 1 ligand (65L), 2 pockets (best druggability 0.66). MolNFT v1 #189390 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VDU
- Type
- protein
- Length
- 291 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2
- EC
- 2.7.11.22
- UniProt
- P24941
- Ligands
- 65L
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 291 | 37% helix, 17% strand | P24941 |
Ligands and binding sites
- 65L · [1-[3-fluoranyl-4-[(2-piperidin-4-yloxy-1,6-naphthyridin-7-yl)amino]phenyl]pyrazol-3-yl]methanol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.66 | 0.81 | 35 | 65L |
| 2 | 81 | 0.38 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 7VDU · The structure of cyclin-dependent kinase 2 (CDK2) in complex with Compound 1 · 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 0.94
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 7VDU · PDBe 7VDU · UniProt P24941
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