MolNFT v1 · #58912 · protein
Structure of phosphorylated THR160 CDK2/CYCLIN a in complex with the inhibitor meriolin 3
3BHT · Cell division protein kinase 2: “Structure of phosphorylated THR160 CDK2/CYCLIN a in complex with the inhibitor meriolin 3”. X-ray diffraction, 2 ligands (MFR, MG), 12 pockets (best druggability 0.80). MolNFT v1 #58912 on GenesisL1…
- PDB
- 3BHT
- Type
- protein
- Length
- 1,093 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P30274
- Ligands
- MFR, MG
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 262 | 68% helix, 0% strand | P30274 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 271 | 35% helix, 19% strand | P24941 |
Ligands and binding sites
- MFR · 4-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
- SGM · Monothioglycerol · additive · 3 copies · chains B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.80 | 0.99 | 22 | empty |
| 2 | 113 | 0.80 | 0.99 | 22 | empty |
| 3 | 1030 | 0.78 | 0.80 | 112 | empty |
| 4 | 226 | 0.69 | 0.85 | 24 | MFR |
| 5 | 206 | 0.67 | 0.84 | 24 | MFR |
Interfaces
5 interfaces between chains.
- C–D · 1926 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1873 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 511 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 110 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 3BHT · Structure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor meriolin 3 · the same entry in another collection · chain D against D, TM-score 1.00
- P30274 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P30274) · 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 0.91
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 P30274
- Elsewhere: RCSB PDB 3BHT · PDBe 3BHT · UniProt P24941 · UniProt P30274
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