Table 4.
Classification of Human Kinase Domain Structures Predicted by AlphaFold2.
| Spatial label | Dihedral label | Other names | #AlphaFold2 chains | AlphaFold2 percentage | #PDB chains | PDB percentage | #PDB Apo chains | PDB Apo percentage |
|---|---|---|---|---|---|---|---|---|
| DFGin | BLAminus | Active | 351 | 70.8 | 3839 | 53.5 | 512 | 55.2 |
| BLBplus | SRC-inactive | 62 | 12.5 | 649 | 9.0 | 55 | 5.9 | |
| ABAminus | Active-like | 16 | 3.2 | 621 | 8.7 | 56 | 6.0 | |
| BLBminus | 29 | 5.8 | 230 | 3.2 | 37 | 4.0 | ||
| BLAplus | FGFR-inactive | 6 | 1.2 | 205 | 2.9 | 24 | 2.6 | |
| BLBtrans | CDK-inactive | 2 | 0.4 | 197 | 2.7 | 12 | 1.3 | |
| None | 8 | 1.6 | 417 | 5.8 | 80 | 8.6 | ||
| DFGinter | BABtrans | 0 | 0.0 | 20 | 0.3 | 5 | 0.5 | |
| None | AURKA-inactive | 8 | 1.6 | 139 | 1.9 | 28 | 3.0 | |
| DFGout | BBAminus | Type-2 binding | 6 | 1.2 | 422 | 5.9 | 18 | 1.9 |
| None | DFGout-like | 5 | 1.0 | 226 | 3.1 | 54 | 5.8 | |
| None | None | 3 | 0.6 | 212 | 3.0 | 46 | 5.0 | |
| Total | - | 496 | 100.0 | 7177 | 100.0 | 927 | 100.0 |
The table compares the state of kinase structures predicted by AlphaFold (available from http://alphafold.ebi.ac.uk) and determined with the standalone Kincore Python script with all chains in the PDB and chains without ligands from the Kincore website (http://dunbrack.fccc.edu/kincore/LIGAND/No_ligand)