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
2003-12-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.480 | 9.620 | 10.240 | 0.810 | 10.250 | 11 |
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 51.769 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.965 | 391.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | IMH |
|---|---|
| Formula: | C11H15N4O4 |
| Molecular weight: | 267.261 g/mol |
| DrugBank ID: | DB06185 |
| Buried Surface Area: | 69.76 % |
| Polar Surface area: | 139.1 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 2.59389 | 18.1032 | 25.8548 |
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- 88 | 4.4 | 0 | Hydrophobic |
| O3' | OH | TYR- 88 | 3.1 | 139.94 | H-Bond (Protein Donor) |
| C5' | CZ | PHE- 200 | 4.23 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 201 | 3.25 | 128.19 | H-Bond (Ligand Donor) |
| N1 | OE1 | GLU- 201 | 3.02 | 154.6 | H-Bond (Ligand Donor) |
| C3' | CE | MET- 219 | 3.7 | 0 | Hydrophobic |
| C2' | CB | MET- 219 | 3.83 | 0 | Hydrophobic |
| O2' | N | MET- 219 | 3.03 | 143.37 | H-Bond (Protein Donor) |
| N7 | OD1 | ASN- 243 | 2.95 | 166.96 | H-Bond (Ligand Donor) |
| O6 | ND2 | ASN- 243 | 3.1 | 165.69 | H-Bond (Protein Donor) |
| O5' | ND1 | HIS- 257 | 2.84 | 152.68 | H-Bond (Ligand Donor) |
