sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 Å
X-ray
2008-12-19
| Name: | Alpha-L-fucosidase, putative |
|---|---|
| ID: | Q9WYE2_THEMA |
| AC: | Q9WYE2 |
| Organism: | Thermotoga maritima |
| Reign: | Bacteria |
| TaxID: | 243274 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 31.019 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.135 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.24 | 54.76 |
| According to VolSite | |
| HET Code: | ZX6 |
|---|---|
| Formula: | C17H24N3O4 |
| Molecular weight: | 334.390 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.68 % |
| Polar Surface area: | 122.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 25.6636 | 5.29192 | 55.7028 |
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 |
| CAA | CE2 | PHE- 32 | 3.96 | 0 | Hydrophobic |
| OAC | NE2 | HIS- 34 | 2.66 | 160.22 | H-Bond (Ligand Donor) |
| CAL | CD2 | LEU- 50 | 4.03 | 0 | Hydrophobic |
| CAV | CE2 | TYR- 64 | 4.42 | 0 | Hydrophobic |
| CAX | CD2 | TYR- 64 | 3.67 | 0 | Hydrophobic |
| CAW | CE2 | TYR- 64 | 4.37 | 0 | Hydrophobic |
| OAE | OE1 | GLU- 66 | 2.78 | 167.37 | H-Bond (Ligand Donor) |
| OAE | NE1 | TRP- 67 | 3.18 | 134.63 | H-Bond (Protein Donor) |
| OAD | NE1 | TRP- 67 | 2.78 | 142.33 | H-Bond (Protein Donor) |
| OAC | NE2 | HIS- 128 | 2.83 | 161.87 | H-Bond (Protein Donor) |
| OAD | NE2 | HIS- 129 | 2.72 | 153.15 | H-Bond (Ligand Donor) |
| CAA | CH2 | TRP- 222 | 4.43 | 0 | Hydrophobic |
| NAN | OD2 | ASP- 224 | 3.81 | 0 | Ionic (Ligand Cationic) |
| NAN | OD1 | ASP- 224 | 2.76 | 0 | Ionic (Ligand Cationic) |
| NAN | OD1 | ASP- 224 | 2.76 | 160.65 | H-Bond (Ligand Donor) |
| CAI | SD | MET- 225 | 3.74 | 0 | Hydrophobic |
| CAH | CD | ARG- 254 | 3.79 | 0 | Hydrophobic |
| NAN | OE2 | GLU- 266 | 2.98 | 150.94 | H-Bond (Ligand Donor) |
| NAN | OE2 | GLU- 266 | 2.98 | 0 | Ionic (Ligand Cationic) |
| NAN | OE1 | GLU- 266 | 3.23 | 0 | Ionic (Ligand Cationic) |
| CAA | CZ | PHE- 290 | 3.73 | 0 | Hydrophobic |
| CAV | CD1 | PHE- 290 | 3.82 | 0 | Hydrophobic |
