sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2009-05-31
| Name: | Vascular endothelial growth factor receptor 1 |
|---|---|
| ID: | VGFR1_HUMAN |
| AC: | P17948 |
| 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: | 27.851 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.436 | 752.625 |
| % Hydrophobic | % Polar |
|---|---|
| 56.95 | 43.05 |
| According to VolSite | |
| HET Code: | 8ST |
|---|---|
| Formula: | C19H16ClN3O |
| Molecular weight: | 337.803 g/mol |
| DrugBank ID: | DB07288 |
| Buried Surface Area: | 75.31 % |
| Polar Surface area: | 54.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 4.72946 | 17.793 | 33.3525 |
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 |
| C24 | CD1 | LEU- 833 | 4.2 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 841 | 3.94 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 841 | 4.42 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 841 | 4.47 | 0 | Hydrophobic |
| C4 | CB | ALA- 859 | 4.26 | 0 | Hydrophobic |
| C19 | CB | ALA- 859 | 4.18 | 0 | Hydrophobic |
| C5 | CB | LYS- 861 | 3.31 | 0 | Hydrophobic |
| C11 | CG | GLU- 878 | 3.97 | 0 | Hydrophobic |
| N9 | OE2 | GLU- 878 | 2.8 | 126.33 | H-Bond (Ligand Donor) |
| C1 | CD1 | LEU- 882 | 4.17 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 882 | 3.86 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 891 | 4.14 | 0 | Hydrophobic |
| C15 | CB | VAL- 892 | 4.22 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 892 | 4.16 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 907 | 3.91 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 909 | 4.07 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 909 | 3.53 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 909 | 3.46 | 0 | Hydrophobic |
| N22 | N | CYS- 912 | 2.93 | 157.12 | H-Bond (Protein Donor) |
| CL16 | CD1 | LEU- 1013 | 3.53 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 1029 | 3.48 | 0 | Hydrophobic |
| C18 | SG | CYS- 1039 | 4.5 | 0 | Hydrophobic |
| O8 | N | ASP- 1040 | 2.84 | 170.74 | H-Bond (Protein Donor) |
| C11 | CB | ASP- 1040 | 3.76 | 0 | Hydrophobic |
| C18 | CZ | PHE- 1041 | 3.77 | 0 | Hydrophobic |
