sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2003-11-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.160 | 8.660 | 8.570 | 0.430 | 9.340 | 4 |
| Name: | Purine nucleoside phosphorylase |
|---|---|
| ID: | PNPH_BOVIN |
| AC: | P55859 |
| Organism: | Bos taurus |
| Reign: | Eukaryota |
| TaxID: | 9913 |
| EC Number: | 2.4.2.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 22.941 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.621 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 44.12 | 55.88 |
| According to VolSite | |
| HET Code: | HA1 |
|---|---|
| Formula: | C10H12F2N5O4P |
| Molecular weight: | 335.204 g/mol |
| DrugBank ID: | DB04260 |
| Buried Surface Area: | 73.72 % |
| Polar Surface area: | 158.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 73.5792 | 45.084 | 50.0545 |
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 |
| F15 | CB | SER- 33 | 4.26 | 0 | Hydrophobic |
| O2P | N | SER- 33 | 3.28 | 156.74 | H-Bond (Protein Donor) |
| O2P | OG | SER- 33 | 3.21 | 164.76 | H-Bond (Protein Donor) |
| O3P | CZ | ARG- 84 | 3.99 | 0 | Ionic (Protein Cationic) |
| O3P | NH1 | ARG- 84 | 2.96 | 151.05 | H-Bond (Protein Donor) |
| O3P | NE2 | HIS- 86 | 2.91 | 170.45 | H-Bond (Protein Donor) |
| F16 | CE2 | TYR- 88 | 4.35 | 0 | Hydrophobic |
| C10 | CB | ALA- 116 | 4.37 | 0 | Hydrophobic |
| C13 | CB | ALA- 116 | 4.16 | 0 | Hydrophobic |
| O2P | N | ALA- 116 | 3.17 | 159.09 | H-Bond (Protein Donor) |
| C11 | CZ | PHE- 200 | 4.42 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 201 | 2.63 | 162.91 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 201 | 2.62 | 154.5 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 201 | 3.32 | 128.69 | H-Bond (Ligand Donor) |
| C12 | SD | MET- 219 | 4.23 | 0 | Hydrophobic |
| F16 | CB | MET- 219 | 3.93 | 0 | Hydrophobic |
| F16 | CB | SER- 220 | 4.1 | 0 | Hydrophobic |
| O1P | OG | SER- 220 | 2.69 | 135.24 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 243 | 3.09 | 146.83 | H-Bond (Protein Donor) |
| O1P | O | HOH- 475 | 2.73 | 155.77 | H-Bond (Protein Donor) |
