sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2012-03-22
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.790 | 9.790 | 9.790 | 0.000 | 9.790 | 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 |
|---|---|
| B | 3 % |
| C | 97 % |
| B-Factor: | 27.686 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.747 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 52.78 | 47.22 |
| According to VolSite | |
| HET Code: | IM5 |
|---|---|
| Formula: | C12H18N5O3 |
| Molecular weight: | 280.303 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.48 % |
| Polar Surface area: | 128.17 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -12.2512 | 2.2927 | -33.2379 |
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 |
| C4' | CB | SER- 33 | 4.42 | 0 | Hydrophobic |
| C3' | CE2 | TYR- 88 | 4.13 | 0 | Hydrophobic |
| O3' | OH | TYR- 88 | 2.61 | 150.25 | H-Bond (Protein Donor) |
| C3' | CE1 | PHE- 159 | 3.77 | 0 | Hydrophobic |
| C4' | CZ | PHE- 159 | 4.11 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 159 | 3.67 | 0 | Hydrophobic |
| C5' | CZ | PHE- 200 | 3.9 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 201 | 2.83 | 171.95 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 201 | 2.83 | 175.38 | H-Bond (Ligand Donor) |
| C3' | SD | MET- 219 | 3.86 | 0 | Hydrophobic |
| O6 | ND2 | ASN- 243 | 2.97 | 176.63 | H-Bond (Protein Donor) |
| N7 | OD1 | ASN- 243 | 2.84 | 164.49 | H-Bond (Ligand Donor) |
| C5' | CB | FT6- 257 | 4.22 | 0 | Hydrophobic |
