Research workbench
Structure of human THR160-phospho CDK2/CYCLIN a complexed with a 2-arylamino-4-cyclohexylmethyl-5-nitroso-6-aminopyrimidine inhibitor
Analyse Structure of human THR160-phospho CDK2/CYCLIN a complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OGU
- Type
- protein
- Length
- 1,078 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
- ST8
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 297 | 35% helix, 16% strand | P24941 |
| B | Cyclin A2 | protein | 253 | 69% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 273 | 36% helix, 19% strand | P24941 |
| D | Cyclin A2 | protein | 255 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- ST8 · 4-{[4-amino-6-(cyclohexylmethoxy)-5-nitrosopyrimidin-2-yl]amino}benzamide · ligand · 2 copies · chains A, C
- SGM · Monothioglycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.98 | 23 | empty |
| 2 | 122 | 0.80 | 0.98 | 25 | empty |
| 3 | 919 | 0.76 | 0.79 | 90 | empty |
| 4 | 213 | 0.67 | 0.85 | 26 | ST8 |
| 5 | 240 | 0.66 | 0.83 | 29 | ST8 |
Interfaces
5 interfaces between chains.
- C–D · 1664 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1584 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 575 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 550 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 115 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 1OGU · Structure of human THR160-phospho CDK2/CYCLIN a complexed with a… · the same entry in another collection · chain C against C, 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 1OGU · PDBe 1OGU · UniProt P24941 · UniProt P20248
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