sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2008-02-08
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.540 | 8.540 | 8.540 | 0.000 | 8.540 | 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: | 26.784 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.224 | 1488.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.56 | 44.44 |
| According to VolSite | |
| HET Code: | XIN |
|---|---|
| Formula: | C31H34N5O4 |
| Molecular weight: | 540.633 g/mol |
| DrugBank ID: | DB09079 |
| Buried Surface Area: | 43.22 % |
| Polar Surface area: | 95.42 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 20.7638 | 67.0597 | 29.9687 |
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 |
| C13 | CB | LEU- 840 | 3.67 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 840 | 3.87 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 848 | 4.16 | 0 | Hydrophobic |
| C17 | CB | VAL- 848 | 4.45 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 848 | 4.14 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 848 | 4.04 | 0 | Hydrophobic |
| N39 | OE1 | GLU- 850 | 3.2 | 153.46 | H-Bond (Ligand Donor) |
| N39 | OE2 | GLU- 850 | 3.3 | 145.06 | H-Bond (Ligand Donor) |
| N39 | OE1 | GLU- 850 | 3.2 | 0 | Ionic (Ligand Cationic) |
| N39 | OE2 | GLU- 850 | 3.3 | 0 | Ionic (Ligand Cationic) |
| O26 | NZ | LYS- 868 | 2.76 | 140.19 | H-Bond (Protein Donor) |
| C28 | CD1 | LEU- 889 | 4.42 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 899 | 4.2 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 899 | 3.67 | 0 | Hydrophobic |
| C28 | CG1 | VAL- 916 | 3.97 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 916 | 3.5 | 0 | Hydrophobic |
| N9 | O | GLU- 917 | 2.93 | 173.09 | H-Bond (Ligand Donor) |
| O10 | N | CYS- 919 | 2.88 | 176.14 | H-Bond (Protein Donor) |
| C11 | CD2 | LEU- 1035 | 4.07 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 1035 | 3.67 | 0 | Hydrophobic |
| C12 | SG | CYS- 1045 | 3.66 | 0 | Hydrophobic |
