sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 Å
X-ray
2014-02-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.110 | 9.110 | 9.110 | 0.000 | 9.110 | 1 |
| Name: | Receptor tyrosine-protein kinase erbB-3 |
|---|---|
| ID: | ERBB3_HUMAN |
| AC: | P21860 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 51.850 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.279 | 529.875 |
| % Hydrophobic | % Polar |
|---|---|
| 54.78 | 45.22 |
| According to VolSite | |
| HET Code: | DB8 |
|---|---|
| Formula: | C26H30Cl2N5O3 |
| Molecular weight: | 531.454 g/mol |
| DrugBank ID: | DB06616 |
| Buried Surface Area: | 54.01 % |
| 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 |
|---|---|---|
| 50.4627 | 13.7064 | 12.8592 |
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- 696 | 3.54 | 0 | Hydrophobic |
| CAN | CD1 | LEU- 696 | 4.46 | 0 | Hydrophobic |
| CBD | CD1 | LEU- 696 | 3.34 | 0 | Hydrophobic |
| CBC | CD1 | LEU- 696 | 3.54 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 704 | 4.29 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 704 | 4.03 | 0 | Hydrophobic |
| CAL | CG1 | VAL- 704 | 3.93 | 0 | Hydrophobic |
| CAJ | SG | CYS- 721 | 4.12 | 0 | Hydrophobic |
| CAK | SG | CYS- 721 | 4.47 | 0 | Hydrophobic |
| C01 | CB | CYS- 721 | 3.98 | 0 | Hydrophobic |
| CBG | SG | CYS- 721 | 3.68 | 0 | Hydrophobic |
| CBE | SG | CYS- 721 | 3.72 | 0 | Hydrophobic |
| C01 | CB | LYS- 723 | 3.91 | 0 | Hydrophobic |
| CAY | CD | LYS- 723 | 3.65 | 0 | Hydrophobic |
| CAX | CB | LYS- 723 | 3.73 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 766 | 3.64 | 0 | Hydrophobic |
| CAX | CG2 | THR- 768 | 4.24 | 0 | Hydrophobic |
| C01 | CG2 | THR- 768 | 3.52 | 0 | Hydrophobic |
| CAN | CE1 | TYR- 770 | 3.63 | 0 | Hydrophobic |
| NAT | N | LEU- 771 | 3.11 | 160.02 | H-Bond (Protein Donor) |
| CBA | CD1 | LEU- 822 | 3.25 | 0 | Hydrophobic |
| CL2 | CB | ALA- 832 | 3.73 | 0 | Hydrophobic |
| CAI | CB | ASP- 833 | 3.71 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 836 | 3.68 | 0 | Hydrophobic |
