MolNFT v1 · #17118 · protein
Structure of human THR160-phospho CDK2/CYCLIN a complexed with a 6-cyclohexylmethyloxy-2-anilino-purine inhibitor
1OIY · Cell division protein kinase 2: “Structure of human THR160-phospho CDK2/CYCLIN a complexed with a 6-cyclohexylmethyloxy-2-anilino-purine…”. X-ray diffraction, 2 ligands (N41, MG), 12 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1OIY
- Type
- protein
- Length
- 1,107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- N41, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 294 | 35% helix, 17% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 297 | 34% helix, 17% strand | P24941 |
Ligands and binding sites
- N41 · 4-(6-cyclohexylmethoxy-9H-purin-2-ylamino)--benzamide · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains B
- SGM · Monothioglycerol · additive · 2 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.80 | 0.98 | 23 | empty |
| 2 | 110 | 0.79 | 0.98 | 22 | empty |
| 3 | 902 | 0.78 | 0.81 | 82 | empty |
| 4 | 234 | 0.71 | 0.86 | 30 | N41 |
| 5 | 209 | 0.67 | 0.85 | 24 | N41 |
Interfaces
5 interfaces between chains.
- C–D · 1764 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1662 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 481 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 108 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 1OIY · Structure of human Thr160-phospho CDK2/cyclin A complexed with a… · 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 0.92
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 1OIY · PDBe 1OIY · UniProt P24941 · UniProt P20248
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