sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2011-08-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.640 | 8.940 | 8.340 | 1.290 | 10.620 | 5 |
| 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: | 13.780 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.697 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 48.09 | 51.91 |
| According to VolSite | |
| HET Code: | 42Q |
|---|---|
| Formula: | C21H15F4N5O2 |
| Molecular weight: | 445.370 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.69 % |
| Polar Surface area: | 81.07 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 |
|---|---|---|
| -24.9685 | -1.14094 | -10.5153 |
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 |
| C6 | CD1 | LEU- 840 | 4.24 | 0 | Hydrophobic |
| C11 | CB | LEU- 840 | 3.78 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 848 | 4.18 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 848 | 4.16 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 848 | 3.75 | 0 | Hydrophobic |
| C6 | CB | ALA- 866 | 4.23 | 0 | Hydrophobic |
| C22 | CD | LYS- 868 | 3.8 | 0 | Hydrophobic |
| C23 | CB | LYS- 868 | 4.41 | 0 | Hydrophobic |
| F34 | CB | LYS- 868 | 3.52 | 0 | Hydrophobic |
| N27 | OE2 | GLU- 885 | 2.95 | 133.4 | H-Bond (Ligand Donor) |
| N29 | OE2 | GLU- 885 | 2.65 | 141.84 | H-Bond (Ligand Donor) |
| C35 | CG | GLU- 885 | 3.82 | 0 | Hydrophobic |
| C36 | CG2 | ILE- 888 | 3.86 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 889 | 4.28 | 0 | Hydrophobic |
| F45 | CD2 | LEU- 889 | 4.48 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 889 | 3.83 | 0 | Hydrophobic |
| C37 | CD1 | ILE- 892 | 4.12 | 0 | Hydrophobic |
| F45 | CD1 | ILE- 892 | 4.26 | 0 | Hydrophobic |
| F47 | CD1 | ILE- 892 | 4.21 | 0 | Hydrophobic |
| F45 | CG1 | VAL- 898 | 3.45 | 0 | Hydrophobic |
| C39 | CG1 | VAL- 899 | 3.93 | 0 | Hydrophobic |
| F45 | CG1 | VAL- 899 | 4 | 0 | Hydrophobic |
| F34 | CG1 | VAL- 914 | 4.44 | 0 | Hydrophobic |
| F34 | CG1 | VAL- 916 | 3.51 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 916 | 3.73 | 0 | Hydrophobic |
| N2 | N | CYS- 919 | 2.82 | 162.14 | H-Bond (Protein Donor) |
| F47 | CD1 | LEU- 1019 | 3.59 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 1035 | 3.9 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 1035 | 4.29 | 0 | Hydrophobic |
| F46 | CG2 | ILE- 1044 | 3.42 | 0 | Hydrophobic |
| C19 | SG | CYS- 1045 | 3.85 | 0 | Hydrophobic |
| C20 | CB | CYS- 1045 | 3.77 | 0 | Hydrophobic |
| O31 | N | ASP- 1046 | 2.84 | 160.05 | H-Bond (Protein Donor) |
| C35 | CB | ASP- 1046 | 4.25 | 0 | Hydrophobic |
| F46 | CB | ASP- 1046 | 4.27 | 0 | Hydrophobic |
| C39 | CB | ASP- 1046 | 3.87 | 0 | Hydrophobic |
| C11 | CZ | PHE- 1047 | 3.54 | 0 | Hydrophobic |
