sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-04-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.660 | 6.660 | 6.660 | 0.000 | 6.660 | 1 |
| 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 | 5 % |
| B | 95 % |
| B-Factor: | 22.929 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.826 | 894.375 |
| % Hydrophobic | % Polar |
|---|---|
| 39.62 | 60.38 |
| According to VolSite | |
| HET Code: | IFM |
|---|---|
| Formula: | C6H14NO3 |
| Molecular weight: | 148.180 g/mol |
| DrugBank ID: | DB04545 |
| Buried Surface Area: | 76.95 % |
| Polar Surface area: | 77.3 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 10.7943 | -10.463 | 40.3026 |
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 |
| O4 | OD2 | ASP- 127 | 2.79 | 161.34 | H-Bond (Ligand Donor) |
| O4 | OD1 | ASP- 127 | 3.5 | 133.9 | H-Bond (Ligand Donor) |
| O3 | OD1 | ASP- 127 | 2.81 | 142.63 | H-Bond (Ligand Donor) |
| C3 | CZ2 | TRP- 179 | 4.16 | 0 | Hydrophobic |
| O3 | NE1 | TRP- 179 | 2.71 | 148.7 | H-Bond (Protein Donor) |
| N | OE2 | GLU- 235 | 2.77 | 136.33 | H-Bond (Ligand Donor) |
| N | OE1 | GLU- 235 | 3.35 | 151.34 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 235 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 235 | 3.35 | 0 | Ionic (Ligand Cationic) |
| C4 | CZ | PHE- 246 | 4.01 | 0 | Hydrophobic |
| C5 | CZ | TYR- 313 | 4.05 | 0 | Hydrophobic |
| C6 | CE2 | TYR- 313 | 4.16 | 0 | Hydrophobic |
| N | OE2 | GLU- 340 | 2.67 | 154.5 | H-Bond (Ligand Donor) |
| N | OE2 | GLU- 340 | 2.67 | 0 | Ionic (Ligand Cationic) |
| N | OE1 | GLU- 340 | 3.75 | 0 | Ionic (Ligand Cationic) |
| C6 | SG | CYS- 342 | 3.94 | 0 | Hydrophobic |
| O4 | NE1 | TRP- 381 | 2.82 | 139.52 | H-Bond (Protein Donor) |
| C4 | CE2 | TRP- 381 | 4.25 | 0 | Hydrophobic |
| C3 | CZ2 | TRP- 381 | 3.67 | 0 | Hydrophobic |
| O6 | ND2 | ASN- 396 | 3.25 | 166.8 | H-Bond (Protein Donor) |
| C6 | CG1 | VAL- 398 | 4.28 | 0 | Hydrophobic |
