sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 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 |
|---|---|
| A | 85 % |
| B | 3 % |
| I | 3 % |
| J | 9 % |
| B-Factor: | 20.861 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.352 | 2271.375 |
| % Hydrophobic | % Polar |
|---|---|
| 45.47 | 54.53 |
| According to VolSite | |
| HET Code: | 5GP |
|---|---|
| Formula: | C10H12N5O8P |
| Molecular weight: | 361.205 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.23 % |
| 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 |
|---|---|---|
| -22.6642 | 11.3125 | 12.8175 |
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' | CZ | PHE- 7 | 4.5 | 0 | Hydrophobic |
| C1' | CZ | PHE- 7 | 4.49 | 0 | Hydrophobic |
| N2 | O | ARG- 30 | 2.94 | 142.08 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 31 | 3.27 | 128 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 31 | 2.56 | 169.9 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 31 | 2.56 | 144.12 | H-Bond (Ligand Donor) |
| N3 | N | ILE- 32 | 3.36 | 157.49 | H-Bond (Protein Donor) |
| C2' | CG2 | ILE- 32 | 4.44 | 0 | Hydrophobic |
| C4' | CD1 | LEU- 41 | 4.02 | 0 | Hydrophobic |
| C1' | CD1 | LEU- 41 | 3.89 | 0 | Hydrophobic |
| O3P | ND2 | ASN- 88 | 2.85 | 153.22 | H-Bond (Protein Donor) |
| O2P | N | GLU- 96 | 2.81 | 165.57 | H-Bond (Protein Donor) |
| O2P | N | VAL- 97 | 3.09 | 167.85 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 97 | 3.99 | 0 | Hydrophobic |
| O2P | NE2 | HIS- 101 | 3.03 | 122.71 | H-Bond (Protein Donor) |
| O3P | NE2 | HIS- 101 | 3.02 | 141.64 | H-Bond (Protein Donor) |
| O5' | NE2 | HIS- 101 | 2.96 | 149.42 | H-Bond (Protein Donor) |
| O3P | NE2 | HIS- 103 | 2.86 | 169.58 | H-Bond (Protein Donor) |
| O3' | O | HOH- 128 | 2.81 | 179.95 | H-Bond (Protein Donor) |
| N2 | O | HOH- 252 | 3.1 | 125.4 | H-Bond (Ligand Donor) |
