sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2013-03-06
| Name: | GTN Reductase |
|---|---|
| ID: | O31246_RHIRD |
| AC: | O31246 |
| Organism: | Rhizobium radiobacter |
| Reign: | Bacteria |
| TaxID: | 358 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 23.813 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | FMN |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.529 | 317.250 |
| % Hydrophobic | % Polar |
|---|---|
| 37.23 | 62.77 |
| According to VolSite | |
| HET Code: | 1L5 |
|---|---|
| Formula: | C9H9NO2 |
| Molecular weight: | 163.173 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.5 % |
| Polar Surface area: | 45.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -0.848083 | 1.37417 | 9.58533 |
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 |
| C | CB | THR- 25 | 3.78 | 0 | Hydrophobic |
| C7 | CG2 | THR- 25 | 3.94 | 0 | Hydrophobic |
| C | CH2 | TRP- 99 | 3.49 | 0 | Hydrophobic |
| O | NE2 | HIS- 178 | 3.11 | 166.53 | H-Bond (Protein Donor) |
| N | ND2 | ASN- 181 | 3.18 | 147.08 | H-Bond (Protein Donor) |
| O | ND2 | ASN- 181 | 3.28 | 176.68 | H-Bond (Protein Donor) |
