sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2009-07-10
| Name: | Neuropilin-1 |
|---|---|
| ID: | NRP1_HUMAN |
| AC: | O14786 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.564 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.179 | 239.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.52 | 46.48 |
| According to VolSite | |
| HET Code: | 8DR |
|---|---|
| Formula: | C17H19N7O5S3 |
| Molecular weight: | 497.572 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 37.84 % |
| Polar Surface area: | 269.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -4.12862 | -8.74491 | -14.5354 |
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 |
| CB | CZ | TYR- 25 | 3.99 | 0 | Hydrophobic |
| CD | CE1 | TYR- 25 | 3.78 | 0 | Hydrophobic |
| CZ | OD2 | ASP- 48 | 3.8 | 0 | Ionic (Ligand Cationic) |
| CZ | OD1 | ASP- 48 | 3.78 | 0 | Ionic (Ligand Cationic) |
| O | OG1 | THR- 77 | 2.57 | 154.88 | H-Bond (Protein Donor) |
| O | OH | TYR- 81 | 2.76 | 167.19 | H-Bond (Protein Donor) |
| CG | CZ | TYR- 81 | 3.8 | 0 | Hydrophobic |
