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
2014-07-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.590 | 7.060 | 7.080 | 0.860 | 8.820 | 15 |
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 63.337 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.905 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.29 | 43.71 |
| According to VolSite | |
| HET Code: | AXI |
|---|---|
| Formula: | C22H18N4OS |
| Molecular weight: | 386.470 g/mol |
| DrugBank ID: | DB06626 |
| Buried Surface Area: | 63.55 % |
| Polar Surface area: | 95.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 76.4704 | 44.29 | 29.3307 |
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 |
| C01 | CD2 | LEU- 248 | 4.46 | 0 | Hydrophobic |
| C09 | CD1 | LEU- 248 | 3.97 | 0 | Hydrophobic |
| C23 | CB | TYR- 253 | 4.45 | 0 | Hydrophobic |
| C08 | CB | TYR- 253 | 4.49 | 0 | Hydrophobic |
| S24 | CG2 | VAL- 256 | 4.18 | 0 | Hydrophobic |
| C08 | CG1 | VAL- 256 | 3.94 | 0 | Hydrophobic |
| C11 | CB | ALA- 269 | 3.52 | 0 | Hydrophobic |
| O81 | NZ | LYS- 271 | 2.96 | 152.44 | H-Bond (Protein Donor) |
| S24 | CD | LYS- 271 | 4.47 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 315 | 4.09 | 0 | Hydrophobic |
| N15 | O | GLU- 316 | 2.77 | 141.58 | H-Bond (Ligand Donor) |
| N14 | N | MET- 318 | 2.75 | 170.48 | H-Bond (Protein Donor) |
| C19 | CD1 | LEU- 370 | 4.37 | 0 | Hydrophobic |
| C09 | CD2 | LEU- 370 | 4.14 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 370 | 3.37 | 0 | Hydrophobic |
| C19 | CB | ALA- 380 | 3.86 | 0 | Hydrophobic |
| C21 | CB | ASP- 381 | 3.22 | 0 | Hydrophobic |
