sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.720 Å
X-ray
2010-05-17
| Name: | Purine nucleoside phosphoramidase |
|---|---|
| ID: | HINT_ECOLI |
| AC: | P0ACE7 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| E | 96 % |
| F | 4 % |
| B-Factor: | 20.713 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.531 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 49.73 | 50.27 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.37 % |
| Polar Surface area: | 217.22 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 7.07425 | 7.61529 | 64.1928 |
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 |
| C5' | CZ | PHE- 7 | 4 | 0 | Hydrophobic |
| N2 | O | ARG- 30 | 2.97 | 154.58 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 31 | 3.04 | 149.69 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 32 | 3.16 | 149.18 | H-Bond (Protein Donor) |
| C1' | CG2 | ILE- 32 | 4.12 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 41 | 3.99 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 41 | 3.92 | 0 | Hydrophobic |
| O3P | ND2 | ASN- 88 | 3.33 | 156.32 | H-Bond (Protein Donor) |
| O1P | N | GLU- 96 | 3.11 | 154.87 | H-Bond (Protein Donor) |
| O2P | N | GLU- 96 | 3.19 | 127.4 | H-Bond (Protein Donor) |
| O2P | N | VAL- 97 | 2.81 | 156.16 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 97 | 3.5 | 0 | Hydrophobic |
| O3P | NE2 | HIS- 103 | 2.8 | 163.42 | H-Bond (Protein Donor) |
| O3P | O | HOH- 121 | 2.88 | 173.21 | H-Bond (Protein Donor) |
