sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.810 Å
X-ray
2010-11-18
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.400 | 8.400 | 8.400 | 0.000 | 8.400 | 3 |
| 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 |
|---|---|
| B | 83 % |
| C | 17 % |
| B-Factor: | 73.668 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.966 | 1647.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.08 | 54.92 |
| According to VolSite | |
| HET Code: | VX6 |
|---|---|
| Formula: | C23H29N8OS |
| Molecular weight: | 465.594 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.34 % |
| Polar Surface area: | 128.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -84.4582 | 5.87967 | -18.9433 |
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 |
| C3 | CD1 | LEU- 294 | 4.33 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 294 | 3.77 | 0 | Hydrophobic |
| S23 | CG | TYR- 299 | 3.95 | 0 | Hydrophobic |
| C29 | CD1 | TYR- 299 | 3.48 | 0 | Hydrophobic |
| C24 | CB | TYR- 299 | 3.92 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 302 | 4.03 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 302 | 3.92 | 0 | Hydrophobic |
| C21 | CB | ALA- 315 | 4.42 | 0 | Hydrophobic |
| C33 | CD | LYS- 317 | 4.01 | 0 | Hydrophobic |
| C34 | SD | MET- 336 | 4.18 | 0 | Hydrophobic |
| C35 | CE | MET- 336 | 3.84 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 345 | 4.21 | 0 | Hydrophobic |
| C21 | CB | THR- 361 | 4.46 | 0 | Hydrophobic |
| C35 | CG2 | THR- 361 | 3.59 | 0 | Hydrophobic |
| N19 | O | GLU- 362 | 2.94 | 148.22 | H-Bond (Ligand Donor) |
| N14 | O | MET- 364 | 2.88 | 139.94 | H-Bond (Ligand Donor) |
| N20 | N | MET- 364 | 2.82 | 167.18 | H-Bond (Protein Donor) |
| C21 | CD1 | LEU- 416 | 3.46 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 416 | 3.86 | 0 | Hydrophobic |
| N30 | OD1 | ASP- 427 | 2.75 | 155.04 | H-Bond (Ligand Donor) |
| C3 | SD | MET- 483 | 3.92 | 0 | Hydrophobic |
