sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2011-10-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.680 | 9.870 | 10.140 | 0.760 | 10.540 | 16 |
| 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: | 38.767 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.203 | 1127.250 |
| % Hydrophobic | % Polar |
|---|---|
| 54.49 | 45.51 |
| According to VolSite | |
| HET Code: | DB8 |
|---|---|
| Formula: | C26H30Cl2N5O3 |
| Molecular weight: | 531.454 g/mol |
| DrugBank ID: | DB06616 |
| Buried Surface Area: | 53.59 % |
| Polar Surface area: | 84.08 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -1.56503 | 13.4798 | -49.948 |
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 |
| CAA | CB | LEU- 248 | 3.63 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 248 | 4.24 | 0 | Hydrophobic |
| CBD | CD1 | LEU- 248 | 3.68 | 0 | Hydrophobic |
| CBC | CD1 | LEU- 248 | 3.71 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 256 | 4.19 | 0 | Hydrophobic |
| CAJ | CG1 | VAL- 256 | 4 | 0 | Hydrophobic |
| CAJ | CB | ALA- 269 | 4.44 | 0 | Hydrophobic |
| C01 | CB | ALA- 269 | 4 | 0 | Hydrophobic |
| CBA | CB | ALA- 269 | 4.07 | 0 | Hydrophobic |
| CAI | CD | LYS- 271 | 4.14 | 0 | Hydrophobic |
| CAX | CB | LYS- 271 | 3.75 | 0 | Hydrophobic |
| C01 | CB | LYS- 271 | 4.22 | 0 | Hydrophobic |
| CL1 | CD | LYS- 271 | 3.44 | 0 | Hydrophobic |
| CL1 | SD | MET- 290 | 4.18 | 0 | Hydrophobic |
| CL1 | CG2 | ILE- 313 | 3.47 | 0 | Hydrophobic |
| C01 | CG2 | ILE- 313 | 4.08 | 0 | Hydrophobic |
| CAX | CG2 | THR- 315 | 4.19 | 0 | Hydrophobic |
| C01 | CG2 | THR- 315 | 3.31 | 0 | Hydrophobic |
| CAN | CZ | PHE- 317 | 3.39 | 0 | Hydrophobic |
| CAK | CB | MET- 318 | 4.46 | 0 | Hydrophobic |
| NAT | N | MET- 318 | 2.86 | 156.05 | H-Bond (Protein Donor) |
| CBE | CD1 | LEU- 370 | 3.64 | 0 | Hydrophobic |
| CBG | CD2 | LEU- 370 | 4.16 | 0 | Hydrophobic |
| CL2 | CB | ALA- 380 | 4.35 | 0 | Hydrophobic |
| CL2 | CE2 | PHE- 382 | 3.43 | 0 | Hydrophobic |
| CAI | CB | PHE- 382 | 4.12 | 0 | Hydrophobic |
| CAI | CD2 | PHE- 382 | 3.19 | 0 | Hydrophobic |
| CL1 | CB | PHE- 382 | 3.62 | 0 | Hydrophobic |
