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
2006-04-20
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.050 | 9.480 | 10.220 | 1.390 | 10.800 | 22 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 33.395 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.122 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 51.83 | 48.17 |
| According to VolSite | |
| HET Code: | 1N1 |
|---|---|
| Formula: | C22H27ClN7O2S |
| Molecular weight: | 489.013 g/mol |
| DrugBank ID: | DB01254 |
| Buried Surface Area: | 55.45 % |
| Polar Surface area: | 135.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 44.5999 | 79.7574 | 39.5991 |
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 | 3.92 | 0 | Hydrophobic |
| C15 | CB | LEU- 248 | 3.66 | 0 | Hydrophobic |
| S | CG1 | VAL- 256 | 4.08 | 0 | Hydrophobic |
| S | CB | ALA- 269 | 4.28 | 0 | Hydrophobic |
| CL | CB | ALA- 269 | 4.18 | 0 | Hydrophobic |
| C7 | CD | LYS- 271 | 4.29 | 0 | Hydrophobic |
| CL | CB | LYS- 271 | 3.46 | 0 | Hydrophobic |
| C7 | CG | GLU- 286 | 4.21 | 0 | Hydrophobic |
| C8 | SD | MET- 290 | 3.94 | 0 | Hydrophobic |
| C7 | CE | MET- 290 | 3.5 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 299 | 3.38 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 313 | 3.47 | 0 | Hydrophobic |
| N2 | OG1 | THR- 315 | 2.84 | 145.69 | H-Bond (Ligand Donor) |
| C5 | CG2 | THR- 315 | 3.58 | 0 | Hydrophobic |
| C5 | CG2 | THR- 315 | 3.58 | 0 | Hydrophobic |
| N | O | MET- 318 | 2.86 | 154.72 | H-Bond (Ligand Donor) |
| N1 | N | MET- 318 | 2.86 | 165.78 | H-Bond (Protein Donor) |
| C10 | CD1 | LEU- 370 | 4.29 | 0 | Hydrophobic |
| S | CD1 | LEU- 370 | 3.99 | 0 | Hydrophobic |
| C10 | CB | ALA- 380 | 3.31 | 0 | Hydrophobic |
| N3 | O | HOH- 620 | 3.4 | 151.51 | H-Bond (Protein Donor) |
