sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2007-10-18
| 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: | 20.857 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.379 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.13 | 34.87 |
| According to VolSite | |
| HET Code: | 2RL |
|---|---|
| Formula: | C26H22ClN3O5 |
| Molecular weight: | 491.923 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.04 % |
| Polar Surface area: | 82.15 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 61.6083 | 48.3555 | 16.9935 |
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 | CB | LEU- 840 | 3.85 | 0 | Hydrophobic |
| C49 | CB | LEU- 840 | 4.27 | 0 | Hydrophobic |
| C53 | CD2 | LEU- 840 | 4.27 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 840 | 4.13 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 840 | 4.01 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 848 | 3.8 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 848 | 4.06 | 0 | Hydrophobic |
| C9 | CB | ALA- 866 | 3.48 | 0 | Hydrophobic |
| C14 | CD | LYS- 868 | 4.45 | 0 | Hydrophobic |
| C27 | CD | LYS- 868 | 4.28 | 0 | Hydrophobic |
| C27 | CG | GLU- 885 | 4.1 | 0 | Hydrophobic |
| C43 | CG | GLU- 885 | 4.45 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 889 | 3.82 | 0 | Hydrophobic |
| C39 | CD2 | LEU- 889 | 3.67 | 0 | Hydrophobic |
| CL48 | CD1 | ILE- 892 | 3.78 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 899 | 4.28 | 0 | Hydrophobic |
| C39 | CG1 | VAL- 899 | 4.21 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 914 | 4.08 | 0 | Hydrophobic |
| C14 | CG2 | THR- 916 | 4.27 | 0 | Hydrophobic |
| C26 | CG2 | THR- 916 | 3.74 | 0 | Hydrophobic |
| C53 | CZ | PHE- 918 | 3.69 | 0 | Hydrophobic |
| C2 | CB | CYS- 919 | 4.32 | 0 | Hydrophobic |
| N7 | N | CYS- 919 | 2.87 | 150.86 | H-Bond (Protein Donor) |
| CL48 | CD1 | LEU- 1019 | 3.59 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 1035 | 4.37 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 1035 | 3.64 | 0 | Hydrophobic |
| C16 | CB | CYS- 1045 | 3.78 | 0 | Hydrophobic |
| C17 | SG | CYS- 1045 | 4.2 | 0 | Hydrophobic |
| O36 | N | ASP- 1046 | 2.7 | 149.34 | H-Bond (Protein Donor) |
| C39 | CB | ASP- 1046 | 4.45 | 0 | Hydrophobic |
| C43 | CB | ASP- 1046 | 3.75 | 0 | Hydrophobic |
| C49 | CE2 | PHE- 1047 | 3.58 | 0 | Hydrophobic |
