MolNFT v1 · #150459 · protein
CDK2/CYCLINA in complex with flavopiridol
6GUB · Cyclin-dependent kinase 2: “CDK2/CYCLINA in complex with flavopiridol”. X-ray diffraction, 1 ligand (F9Z), 16 pockets (best druggability 0.81). MolNFT v1 #150459 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GUB
- Type
- protein
- Length
- 1,108 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, P30274
- Ligands
- F9Z
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 294 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin-A2 | protein | 261 | 64% helix, 0% strand | P30274 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 292 | 33% helix, 18% strand | P24941 |
Ligands and binding sites
- F9Z · 2-(2-chlorophenyl)-8-[(3~{R},4~{R})-1-methyl-3-oxidanyl-piperidin-4-yl]-5,7-bis(oxidanyl)chromen-4-one · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.81 | 0.98 | 25 | empty |
| 2 | 133 | 0.81 | 0.98 | 22 | empty |
| 3 | 1165 | 0.76 | 0.78 | 108 | empty |
| 4 | 220 | 0.69 | 0.86 | 27 | F9Z |
| 5 | 248 | 0.66 | 0.83 | 25 | F9Z |
Interfaces
5 interfaces between chains.
- C–D · 1892 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1821 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 522 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 483 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 6GUB · CDK2/CyclinA in complex with Flavopiridol · 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 6GUB · PDBe 6GUB · UniProt P24941 · UniProt P30274
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