sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2010-12-09
| Name: | Chitinase A |
|---|---|
| ID: | Q9AMP1_VIBHA |
| AC: | Q9AMP1 |
| Organism: | Vibrio harveyi |
| Reign: | Bacteria |
| TaxID: | 669 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 9.849 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.836 | 1329.750 |
| % Hydrophobic | % Polar |
|---|---|
| 47.21 | 52.79 |
| According to VolSite | |
| HET Code: | DM5 |
|---|---|
| Formula: | C26H26NO9 |
| Molecular weight: | 496.486 g/mol |
| DrugBank ID: | DB01177 |
| Buried Surface Area: | 37.2 % |
| Polar Surface area: | 183.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 18.7087 | -10.9349 | 21.4864 |
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 |
| C10 | CH2 | TRP- 275 | 4.45 | 0 | Hydrophobic |
| C2' | CH2 | TRP- 275 | 4.16 | 0 | Hydrophobic |
| C1 | CB | TRP- 275 | 3.74 | 0 | Hydrophobic |
| N3' | O | GLY- 321 | 2.94 | 165.33 | H-Bond (Ligand Donor) |
| C15 | CB | ASP- 392 | 4.31 | 0 | Hydrophobic |
| C10 | CD2 | TRP- 397 | 3.43 | 0 | Hydrophobic |
| C11 | CE2 | TRP- 397 | 3.53 | 0 | Hydrophobic |
| C12 | CZ2 | TRP- 397 | 4.37 | 0 | Hydrophobic |
| C14 | CZ2 | TRP- 397 | 4.05 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 397 | 3.98 | 0 | Hydrophobic |
| C14 | CD2 | TYR- 435 | 3.35 | 0 | Hydrophobic |
