sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2012-01-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.230 | 8.230 | 8.230 | 0.000 | 8.230 | 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: | 18.373 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.357 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 77.42 | 22.58 |
| According to VolSite | |
| HET Code: | AXI |
|---|---|
| Formula: | C22H18N4OS |
| Molecular weight: | 386.470 g/mol |
| DrugBank ID: | DB06626 |
| Buried Surface Area: | 72.06 % |
| Polar Surface area: | 95.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 20.8237 | 25.5351 | 39.4596 |
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 |
| C10 | CD1 | LEU- 840 | 4.49 | 0 | Hydrophobic |
| C01 | CD2 | LEU- 840 | 4.24 | 0 | Hydrophobic |
| C08 | CG1 | VAL- 848 | 4.1 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 848 | 3.63 | 0 | Hydrophobic |
| C19 | CB | ALA- 866 | 4.46 | 0 | Hydrophobic |
| C11 | CB | ALA- 866 | 3.59 | 0 | Hydrophobic |
| C20 | CB | LYS- 868 | 3.5 | 0 | Hydrophobic |
| N82 | OE2 | GLU- 885 | 2.7 | 155.9 | H-Bond (Ligand Donor) |
| C22 | CD1 | LEU- 889 | 4.24 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 899 | 4.1 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 914 | 3.98 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 916 | 4.01 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 916 | 3.54 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 916 | 3.49 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 916 | 3.86 | 0 | Hydrophobic |
| N15 | O | GLU- 917 | 2.88 | 157.94 | H-Bond (Ligand Donor) |
| N14 | N | CYS- 919 | 2.97 | 150.78 | H-Bond (Protein Donor) |
| C09 | CD2 | LEU- 1035 | 3.84 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 1035 | 3.35 | 0 | Hydrophobic |
| S24 | CB | CYS- 1045 | 3.91 | 0 | Hydrophobic |
| C07 | SG | CYS- 1045 | 4.16 | 0 | Hydrophobic |
| O81 | N | ASP- 1046 | 2.97 | 172.49 | H-Bond (Protein Donor) |
| C08 | CZ | PHE- 1047 | 3.39 | 0 | Hydrophobic |
