MolNFT v1 · #81264 · protein
Human cyclin dependent kinase 2 (CDK2) bound to azabenzimidazole derivative
3ULI · Cyclin-dependent kinase 2: “Human cyclin dependent kinase 2 (CDK2) bound to azabenzimidazole derivative”. X-ray diffraction, 1 ligand (1N3), 2 pockets (best druggability 0.69). MolNFT v1 #81264 on GenesisL1: 3D structure, binding…
- PDB
- 3ULI
- Type
- protein
- Length
- 286 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
- 1N3
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 286 | 34% helix, 16% strand | P24941 |
Ligands and binding sites
- 1N3 · 1-(aminomethyl)-N-(3-{[6-bromo-2-(4-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-7-yl]amino}propyl)cyclopropanecarboxamide · 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 | 397 | 0.69 | 0.81 | 40 | 1N3 |
| 2 | 55 | 0.36 | 0.79 | 17 | empty |
Compared structures
- 3ULI · Human Cyclin Dependent Kinase 2 (CDK2) bound to azabenzimidazole derivative · 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 0.96
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 3ULI · PDBe 3ULI · UniProt P24941
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