MolNFT v1 · #159475 · protein
CDK2 in complex with CPD14 (5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro- 4H-PYRAZOLO[1,5-A]AZEPIN-3-yl)-N-(5-(4-methylpiperazin-1-YL)PYRIDIN- 2-YL)PYRIMIDIN-2-amine)
6OQI · Cyclin-dependent kinase 2: “CDK2 in complex with CPD14 (5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro…”. X-ray diffraction, 1 ligand (N14), 3 pockets (best druggability 0.71). MolNFT v1 #159475 on GenesisL1: 3D structure, binding sites…
- PDB
- 6OQI
- Type
- protein
- Length
- 290 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
- N14
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 290 | 34% helix, 17% strand | P24941 |
Ligands and binding sites
- N14 · 5-fluoro-N-[5-(4-methylpiperazin-1-yl)pyridin-2-yl]-4-[(4S)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.71 | 0.83 | 40 | N14 |
| 2 | 51 | 0.30 | 0.76 | 12 | empty |
| 3 | 52 | 0.29 | 0.75 | 12 | empty |
Compared structures
- 6OQI · CDK2 in complex with Cpd14 (5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azep… · 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 6OQI · PDBe 6OQI · UniProt P24941
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