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
2012-01-26
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.520 | 8.600 | 8.680 | 0.670 | 9.700 | 10 |
| Name: | Vascular endothelial growth factor receptor 2 |
|---|---|
| ID: | VGFR2_HUMAN |
| AC: | P35968 |
| 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: | 50.363 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.204 | 263.250 |
| % Hydrophobic | % Polar |
|---|---|
| 69.23 | 30.77 |
| According to VolSite | |
| HET Code: | B49 |
|---|---|
| Formula: | C22H28FN4O2 |
| Molecular weight: | 399.482 g/mol |
| DrugBank ID: | DB01268 |
| Buried Surface Area: | 49.2 % |
| Polar Surface area: | 78.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 50.0728 | -2.07021 | -14.8793 |
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 |
| C4 | CD2 | LEU- 840 | 3.79 | 0 | Hydrophobic |
| C3 | CB | LEU- 840 | 3.93 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 848 | 4.09 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 848 | 4.03 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 899 | 3.75 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 916 | 3.49 | 0 | Hydrophobic |
| N24 | O | GLU- 917 | 2.93 | 165.55 | H-Bond (Ligand Donor) |
| C4 | CE1 | PHE- 918 | 3.72 | 0 | Hydrophobic |
| O27 | N | CYS- 919 | 2.92 | 161.62 | H-Bond (Protein Donor) |
| C17 | CD1 | LEU- 1035 | 3.39 | 0 | Hydrophobic |
| C7 | SG | CYS- 1045 | 4.41 | 0 | Hydrophobic |
| F29 | CB | CYS- 1045 | 3.96 | 0 | Hydrophobic |
| C3 | CZ | PHE- 1047 | 3.64 | 0 | Hydrophobic |
| F29 | CG | PHE- 1047 | 4.11 | 0 | Hydrophobic |
| O28 | O | HOH- 2037 | 3.24 | 180 | H-Bond (Protein Donor) |
