sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2008-09-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.590 | 7.590 | 7.590 | 0.000 | 7.590 | 2 |
| 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: | 32.978 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.398 | 637.875 |
| % Hydrophobic | % Polar |
|---|---|
| 60.85 | 39.15 |
| According to VolSite | |
| HET Code: | 706 |
|---|---|
| Formula: | C22H23N5O |
| Molecular weight: | 373.451 g/mol |
| DrugBank ID: | DB05575 |
| Buried Surface Area: | 73.18 % |
| Polar Surface area: | 78.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 38.0605 | 34.6333 | 12.7408 |
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 |
| C21 | CD1 | LEU- 840 | 3.86 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 848 | 3.92 | 0 | Hydrophobic |
| C16 | CB | ALA- 866 | 3.82 | 0 | Hydrophobic |
| C4 | CB | LYS- 868 | 3.4 | 0 | Hydrophobic |
| N12 | OE2 | GLU- 885 | 3.1 | 139.36 | H-Bond (Ligand Donor) |
| C22 | CG | GLU- 885 | 3.81 | 0 | Hydrophobic |
| C28 | CG2 | ILE- 888 | 4.46 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 889 | 4.05 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 889 | 3.75 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 892 | 3.51 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 899 | 4.26 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 899 | 3.34 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 914 | 4.27 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 916 | 3.98 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 916 | 3.78 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 916 | 3.98 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 916 | 3.89 | 0 | Hydrophobic |
| N19 | N | CYS- 919 | 3.18 | 172.26 | H-Bond (Protein Donor) |
| C2 | CD1 | LEU- 1019 | 4.26 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 1019 | 3.98 | 0 | Hydrophobic |
| C3 | SG | CYS- 1024 | 4.48 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 1035 | 3.47 | 0 | Hydrophobic |
| C2 | CB | ASP- 1046 | 4.43 | 0 | Hydrophobic |
| C24 | CB | ASP- 1046 | 4.5 | 0 | Hydrophobic |
| C26 | CB | ASP- 1046 | 3.6 | 0 | Hydrophobic |
| O11 | N | ASP- 1046 | 3.03 | 170.72 | H-Bond (Protein Donor) |
| C15 | CE2 | PHE- 1047 | 3.74 | 0 | Hydrophobic |
