sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2009-03-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.300 | 7.680 | 8.000 | 0.700 | 8.220 | 5 |
| Name: | Abelson tyrosine-protein kinase 2 |
|---|---|
| ID: | ABL2_HUMAN |
| AC: | P42684 |
| 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: | 15.981 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.044 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.55 | 45.45 |
| According to VolSite | |
| HET Code: | STI |
|---|---|
| Formula: | C29H32N7O |
| Molecular weight: | 494.611 g/mol |
| DrugBank ID: | DB00619 |
| Buried Surface Area: | 66.49 % |
| 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 |
|---|---|---|
| 15.4904 | 9.93178 | 19.6139 |
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 |
| C1 | CG | LEU- 294 | 4.07 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 294 | 3.91 | 0 | Hydrophobic |
| C12 | CB | TYR- 299 | 4.08 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 302 | 3.86 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 302 | 4.29 | 0 | Hydrophobic |
| C5 | CB | ALA- 315 | 4.24 | 0 | Hydrophobic |
| C20 | CB | ALA- 315 | 3.98 | 0 | Hydrophobic |
| C17 | CD | LYS- 317 | 4.3 | 0 | Hydrophobic |
| C18 | CB | LYS- 317 | 3.63 | 0 | Hydrophobic |
| N21 | OE2 | GLU- 332 | 2.91 | 127.38 | H-Bond (Ligand Donor) |
| C25 | CG | GLU- 332 | 4 | 0 | Hydrophobic |
| C17 | SD | MET- 336 | 3.71 | 0 | Hydrophobic |
| C15 | CE | MET- 336 | 4.48 | 0 | Hydrophobic |
| C23 | SD | MET- 336 | 4.15 | 0 | Hydrophobic |
| C25 | CG | MET- 336 | 3.81 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 339 | 4.16 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 345 | 4.08 | 0 | Hydrophobic |
| C29 | CG1 | VAL- 345 | 4.44 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 359 | 3.73 | 0 | Hydrophobic |
| N13 | OG1 | THR- 361 | 3.05 | 132.71 | H-Bond (Ligand Donor) |
| C20 | CG2 | THR- 361 | 3.99 | 0 | Hydrophobic |
| C14 | CG2 | THR- 361 | 3.47 | 0 | Hydrophobic |
| N3 | N | MET- 364 | 2.89 | 167.04 | H-Bond (Protein Donor) |
| N51 | O | ILE- 406 | 2.75 | 140.85 | H-Bond (Ligand Donor) |
| C6 | CD2 | LEU- 416 | 3.92 | 0 | Hydrophobic |
| O29 | N | ASP- 427 | 2.84 | 160.45 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 427 | 3.81 | 0 | Hydrophobic |
