MolNFT v1 · #90622 · protein
Thr 160 phosphorylated CDK2 wt - human cyclin A3 complex with the inhibitor NU6102
4EOR · Cyclin-dependent kinase 2: “Thr 160 phosphorylated CDK2 wt - human cyclin A3 complex with the inhibitor NU6102”. X-ray diffraction, 1 ligand (4SP), 15 pockets (best druggability 0.81). MolNFT v1 #90622 on GenesisL1: 3D structure…
- PDB
- 4EOR
- Type
- protein
- Length
- 1,077 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- 4SP
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 294 | 35% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 66% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 271 | 34% helix, 19% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- 4SP · O6-cyclohexylmethoxy-2-(4'-sulphamoylanilino) purine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.81 | 0.98 | 23 | empty |
| 2 | 117 | 0.80 | 0.98 | 20 | empty |
| 3 | 731 | 0.74 | 0.79 | 59 | empty |
| 4 | 196 | 0.67 | 0.85 | 28 | 4SP |
| 5 | 206 | 0.65 | 0.84 | 29 | 4SP |
Interfaces
5 interfaces between chains.
- C–D · 1714 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1595 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 484 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 61 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4EOR · Thr 160 phosphorylated CDK2 WT - human cyclin A3 complex with the inhibitor NU6102 · 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 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 0.91
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 4EOR · PDBe 4EOR · UniProt P24941 · UniProt P20248
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