sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2011-08-25
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.600 | 4.600 | 4.600 | 0.000 | 4.600 | 1 |
| 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: | 59.402 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.377 | 729.000 |
| % Hydrophobic | % Polar |
|---|---|
| 57.87 | 42.13 |
| According to VolSite | |
| HET Code: | BPK |
|---|---|
| Formula: | C18H17NO3 |
| Molecular weight: | 295.332 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.44 % |
| Polar Surface area: | 55.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -29.0256 | 26.4012 | 16.5209 |
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 | CG2 | VAL- 848 | 4.4 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 848 | 3.64 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 848 | 4.05 | 0 | Hydrophobic |
| C4 | CB | ALA- 866 | 3.99 | 0 | Hydrophobic |
| C12 | CD | LYS- 868 | 3.79 | 0 | Hydrophobic |
| C12 | CG | GLU- 885 | 3.84 | 0 | Hydrophobic |
| C13 | CG | GLU- 885 | 4.25 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 889 | 3.47 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 889 | 4.01 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 889 | 4.18 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 892 | 4.17 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 898 | 3.89 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 914 | 3.8 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 916 | 4.31 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 916 | 3.39 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 1019 | 3.84 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 1035 | 3.92 | 0 | Hydrophobic |
| C2 | CB | CYS- 1045 | 4.01 | 0 | Hydrophobic |
| C7 | SG | CYS- 1045 | 3.57 | 0 | Hydrophobic |
| C13 | CB | ASP- 1046 | 4.44 | 0 | Hydrophobic |
| C16 | CB | ASP- 1046 | 4.11 | 0 | Hydrophobic |
| N8 | N | ASP- 1046 | 3.12 | 165.73 | H-Bond (Protein Donor) |
