sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2006-08-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.160 | 7.470 | 7.460 | 0.850 | 8.960 | 31 |
| Name: | Tyrosine-protein kinase ABL1 |
|---|---|
| ID: | ABL1_HUMAN |
| AC: | P00519 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 41.641 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.310 | 1228.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.12 | 45.88 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 65.14 % |
| Polar Surface area: | 87.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 57.7264 | 15.0275 | 46.2908 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C12 | CD1 | LEU- 248 | 4.18 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 248 | 3.86 | 0 | Hydrophobic |
| C12 | CB | TYR- 253 | 4.24 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 256 | 4.15 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 256 | 3.92 | 0 | Hydrophobic |
| C5 | CB | ALA- 269 | 4.39 | 0 | Hydrophobic |
| C20 | CB | ALA- 269 | 3.89 | 0 | Hydrophobic |
| C17 | CD | LYS- 271 | 3.84 | 0 | Hydrophobic |
| C18 | CB | LYS- 271 | 3.35 | 0 | Hydrophobic |
| N21 | OE2 | GLU- 286 | 2.85 | 143.85 | H-Bond (Ligand Donor) |
| C29 | CG | GLU- 286 | 3.91 | 0 | Hydrophobic |
| C17 | CE | MET- 290 | 3.58 | 0 | Hydrophobic |
| C23 | SD | MET- 290 | 3.83 | 0 | Hydrophobic |
| C29 | CG | MET- 290 | 3.73 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 293 | 3.98 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 299 | 4.28 | 0 | Hydrophobic |
| C25 | CG1 | VAL- 299 | 4.42 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 313 | 3.67 | 0 | Hydrophobic |
| N13 | OG1 | THR- 315 | 3 | 128.51 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 315 | 4.24 | 0 | Hydrophobic |
| C14 | CG2 | THR- 315 | 3.61 | 0 | Hydrophobic |
| N3 | N | MET- 318 | 2.52 | 163.5 | H-Bond (Protein Donor) |
| N51 | O | ILE- 360 | 2.61 | 143.66 | H-Bond (Ligand Donor) |
| C6 | CD2 | LEU- 370 | 3.76 | 0 | Hydrophobic |
| O29 | N | ASP- 381 | 3.18 | 153.69 | H-Bond (Protein Donor) |
| C25 | CB | ASP- 381 | 4 | 0 | Hydrophobic |
