sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.400 Å
X-ray
2007-11-05
| Name: | IAG-nucleoside hydrolase |
|---|---|
| ID: | Q9GPQ4_TRYVI |
| AC: | Q9GPQ4 |
| Organism: | Trypanosoma vivax |
| Reign: | Eukaryota |
| TaxID: | 5699 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 16.152 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.387 | 337.500 |
| % Hydrophobic | % Polar |
|---|---|
| 58.00 | 42.00 |
| According to VolSite | |
| HET Code: | IMH |
|---|---|
| Formula: | C11H15N4O4 |
| Molecular weight: | 267.261 g/mol |
| DrugBank ID: | DB06185 |
| Buried Surface Area: | 76.2 % |
| 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 |
|---|---|---|
| 5.81042 | 23.8278 | -14.8215 |
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 |
| O2' | OD1 | ASP- 14 | 2.83 | 147.34 | H-Bond (Ligand Donor) |
| C5' | SD | MET- 164 | 3.68 | 0 | Hydrophobic |
| C3' | SD | MET- 164 | 3.85 | 0 | Hydrophobic |
| O5' | ND2 | ASN- 173 | 2.93 | 166.78 | H-Bond (Protein Donor) |
| O5' | OE2 | GLU- 184 | 2.62 | 161.98 | H-Bond (Ligand Donor) |
| N4' | OE2 | GLU- 184 | 3.77 | 0 | Ionic (Ligand Cationic) |
| N4' | OD1 | ASN- 186 | 2.98 | 151.02 | H-Bond (Ligand Donor) |
| O3' | ND2 | ASN- 186 | 3.09 | 156.61 | H-Bond (Protein Donor) |
| C5' | CD2 | TRP- 250 | 3.58 | 0 | Hydrophobic |
| C3' | CB | TRP- 250 | 3.98 | 0 | Hydrophobic |
| C2' | CE3 | TRP- 250 | 3.87 | 0 | Hydrophobic |
| O3' | OD1 | ASP- 251 | 2.54 | 167.18 | H-Bond (Ligand Donor) |
| O3' | CA | CA- 318 | 2.52 | 0 | Metal Acceptor |
| O2' | CA | CA- 318 | 2.49 | 0 | Metal Acceptor |
| N4' | O | HOH- 523 | 3.27 | 128.59 | H-Bond (Ligand Donor) |
