sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-03-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.000 | 8.000 | 8.000 | 0.000 | 8.000 | 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: | 24.802 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.692 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 67.36 | 32.64 |
| According to VolSite | |
| HET Code: | 608 |
|---|---|
| Formula: | C24H20N4O2 |
| Molecular weight: | 396.441 g/mol |
| DrugBank ID: | DB07183 |
| Buried Surface Area: | 73.26 % |
| Polar Surface area: | 76.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 38.2031 | 35.4661 | 12.0867 |
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 |
| C8 | CD1 | LEU- 840 | 3.71 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 848 | 3.93 | 0 | Hydrophobic |
| C17 | CB | ALA- 866 | 3.85 | 0 | Hydrophobic |
| C21 | CB | LYS- 868 | 3.65 | 0 | Hydrophobic |
| N2 | OE2 | GLU- 885 | 2.87 | 146.01 | H-Bond (Ligand Donor) |
| C13 | CG | GLU- 885 | 3.65 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 888 | 3.54 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 889 | 4.43 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 889 | 3.77 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 892 | 3.44 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 898 | 4.3 | 0 | Hydrophobic |
| C11 | CB | VAL- 899 | 4.15 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 899 | 4.49 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 914 | 4.33 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 916 | 3.88 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 916 | 4.16 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 916 | 3.7 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 916 | 3.82 | 0 | Hydrophobic |
| N4 | N | CYS- 919 | 3.15 | 174.96 | H-Bond (Protein Donor) |
| C4 | CD2 | LEU- 1019 | 3.72 | 0 | Hydrophobic |
| C2 | CB | CYS- 1024 | 3.7 | 0 | Hydrophobic |
| C3 | SG | CYS- 1024 | 3.79 | 0 | Hydrophobic |
| C6 | CB | HIS- 1026 | 4.49 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 1035 | 3.42 | 0 | Hydrophobic |
| O1 | N | ASP- 1046 | 2.81 | 149.15 | H-Bond (Protein Donor) |
| C13 | CB | ASP- 1046 | 3.53 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 1047 | 3.93 | 0 | Hydrophobic |
