sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-03-12
| Name: | Glucosylceramidase |
|---|---|
| ID: | GLCM_HUMAN |
| AC: | P04062 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.2.1.45 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.175 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.936 | 1586.250 |
| % Hydrophobic | % Polar |
|---|---|
| 48.94 | 51.06 |
| According to VolSite | |
| HET Code: | MT5 |
|---|---|
| Formula: | C15H30N3O4 |
| Molecular weight: | 316.416 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.84 % |
| Polar Surface area: | 110.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 6 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -25.4424 | -17.0607 | -41.3914 |
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 |
| O20 | OD1 | ASP- 127 | 2.65 | 151.53 | H-Bond (Ligand Donor) |
| O22 | OD1 | ASP- 127 | 3.09 | 131.54 | H-Bond (Ligand Donor) |
| O22 | OD2 | ASP- 127 | 2.55 | 162.25 | H-Bond (Ligand Donor) |
| O20 | NE1 | TRP- 179 | 2.87 | 164 | H-Bond (Protein Donor) |
| O18 | ND2 | ASN- 234 | 3.09 | 156.58 | H-Bond (Protein Donor) |
| O16 | OE1 | GLU- 235 | 2.77 | 177.84 | H-Bond (Ligand Donor) |
| C15 | CZ | PHE- 246 | 4.45 | 0 | Hydrophobic |
| C21 | CZ | PHE- 246 | 4.08 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 246 | 4.19 | 0 | Hydrophobic |
| C13 | CZ | TYR- 313 | 4.06 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 313 | 4.06 | 0 | Hydrophobic |
| O18 | OE1 | GLU- 340 | 2.88 | 152.76 | H-Bond (Ligand Donor) |
| O18 | OE2 | GLU- 340 | 3.03 | 137.71 | H-Bond (Ligand Donor) |
| C19 | CZ2 | TRP- 381 | 3.93 | 0 | Hydrophobic |
| C21 | CE2 | TRP- 381 | 4.33 | 0 | Hydrophobic |
| O22 | NE1 | TRP- 381 | 2.94 | 141.13 | H-Bond (Protein Donor) |
