MolNFT v1 · #7071 · protein
The structure of CDK2/CYCLIN a in complex with an oxindole inhibitor
1FVV · Cyclin-dependent kinase 2: “The structure of CDK2/CYCLIN a in complex with an oxindole inhibitor”. X-ray diffraction, 1 ligand (107), 14 pockets (best druggability 0.78). MolNFT v1 #7071 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1FVV
- Type
- protein
- Length
- 1,116 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin a
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- 107
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase 2 (EC 2.7.1.37) | protein | 298 | 32% helix, 16% strand | P24941 |
| B, D | Cyclin a | protein | 260 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 107 · 4-[(7-oxo-7H-thiazolo[5,4-e]indol-8-ylmethyl)-amino]-N-pyridin-2-yl-benzenesulfonamide · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.78 | 0.96 | 23 | empty |
| 2 | 132 | 0.77 | 0.95 | 25 | empty |
| 3 | 872 | 0.76 | 0.79 | 93 | empty |
| 4 | 297 | 0.67 | 0.82 | 40 | 107 |
| 5 | 354 | 0.66 | 0.80 | 49 | 107 |
Interfaces
5 interfaces between chains.
- C–D · 1794 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1768 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 479 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 68 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1FVV · The structure of CDK2/CYCLIN a in complex with an oxindole 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 B against A, TM-score 0.99
- 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 0.92
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 1FVV · PDBe 1FVV · UniProt P24941 · UniProt P20248
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