sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2008-11-13
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | Q9BMI9_SCHMA |
| AC: | Q9BMI9 |
| Organism: | Schistosoma mansoni |
| Reign: | Eukaryota |
| TaxID: | 6183 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 3 % |
| C | 97 % |
| B-Factor: | 32.544 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.547 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 43.96 | 56.04 |
| According to VolSite | |
| HET Code: | ADN |
|---|---|
| Formula: | C10H13N5O4 |
| Molecular weight: | 267.241 g/mol |
| DrugBank ID: | DB00640 |
| Buried Surface Area: | 80.84 % |
| Polar Surface area: | 139.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 14.8214 | 31.641 | 41.1101 |
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 |
| C3' | CE2 | TYR- 90 | 4.15 | 0 | Hydrophobic |
| O3' | OH | TYR- 90 | 2.92 | 144.2 | H-Bond (Protein Donor) |
| C1' | CB | ALA- 118 | 4.29 | 0 | Hydrophobic |
| C5' | CD1 | PHE- 161 | 3.7 | 0 | Hydrophobic |
| C4' | CZ | PHE- 161 | 3.81 | 0 | Hydrophobic |
| C3' | CE1 | PHE- 161 | 3.64 | 0 | Hydrophobic |
| O5' | OH | TYR- 202 | 2.67 | 172.83 | H-Bond (Ligand Donor) |
| C5' | CE2 | TYR- 202 | 3.81 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 203 | 2.53 | 156.66 | H-Bond (Ligand Donor) |
| O2' | N | MET- 221 | 2.91 | 144.92 | H-Bond (Protein Donor) |
| C2' | SD | MET- 221 | 3.89 | 0 | Hydrophobic |
| N7 | ND2 | ASN- 245 | 2.76 | 167.64 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 245 | 2.63 | 152.85 | H-Bond (Ligand Donor) |
| O5' | ND1 | HIS- 259 | 2.66 | 162.84 | H-Bond (Protein Donor) |
