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
2003-10-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.300 | 5.300 | 5.300 | 0.000 | 5.300 | 1 |
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | PNPH_HUMAN |
| AC: | P00491 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 100 % |
| B-Factor: | 38.015 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.870 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.10 | 53.90 |
| According to VolSite | |
| HET Code: | GUN |
|---|---|
| Formula: | C5H5N5O |
| Molecular weight: | 151.126 g/mol |
| DrugBank ID: | DB02377 |
| Buried Surface Area: | 67.02 % |
| Polar Surface area: | 96.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -15.6314 | 88.8699 | -0.396364 |
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 |
| N2 | OE2 | GLU- 201 | 2.8 | 132.31 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 201 | 3.25 | 162.85 | H-Bond (Ligand Donor) |
| N7 | OD1 | ASN- 243 | 2.5 | 165.75 | H-Bond (Ligand Donor) |
| O6 | ND2 | ASN- 243 | 2.81 | 148.21 | H-Bond (Protein Donor) |
