sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2014-08-28
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 40.981 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.476 | 644.625 |
| % Hydrophobic | % Polar |
|---|---|
| 69.63 | 30.37 |
| According to VolSite | |
| HET Code: | AXI |
|---|---|
| Formula: | C22H18N4OS |
| Molecular weight: | 386.470 g/mol |
| DrugBank ID: | DB06626 |
| Buried Surface Area: | 59.13 % |
| 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 |
|---|---|---|
| 24.807 | 126.534 | 15.3409 |
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 |
| C06 | CD2 | LEU- 248 | 4.42 | 0 | Hydrophobic |
| C01 | CB | LEU- 248 | 3.98 | 0 | Hydrophobic |
| C21 | CB | TYR- 253 | 3.66 | 0 | Hydrophobic |
| C08 | CG2 | VAL- 256 | 4.11 | 0 | Hydrophobic |
| C09 | CG1 | VAL- 256 | 4.03 | 0 | Hydrophobic |
| C11 | CB | ALA- 269 | 3.44 | 0 | Hydrophobic |
| C23 | CD | LYS- 271 | 4.35 | 0 | Hydrophobic |
| S24 | CD | LYS- 271 | 4.05 | 0 | Hydrophobic |
| N15 | O | GLU- 316 | 2.93 | 150.42 | H-Bond (Ligand Donor) |
| N14 | N | MET- 318 | 2.84 | 171.27 | H-Bond (Protein Donor) |
| C21 | CB | ASN- 368 | 4.33 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 370 | 4.33 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 370 | 3.29 | 0 | Hydrophobic |
| C20 | CB | ALA- 380 | 3.76 | 0 | Hydrophobic |
| C22 | CB | PHE- 382 | 3.74 | 0 | Hydrophobic |
