sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2013-01-17
| Name: | Strictosidine-O-beta-D-glucosidase |
|---|---|
| ID: | SG1_RAUSE |
| AC: | Q8GU20 |
| Organism: | Rauvolfia serpentina |
| Reign: | Eukaryota |
| TaxID: | 4060 |
| EC Number: | 3.2.1.105 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 38.721 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.870 | 904.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.78 | 55.22 |
| According to VolSite | |
| HET Code: | C1K |
|---|---|
| Formula: | C12H24NO4 |
| Molecular weight: | 246.323 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.79 % |
| Polar Surface area: | 97.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -52.0174 | -29.8309 | 28.0074 |
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 |
| OAB | OE1 | GLN- 57 | 2.88 | 139.36 | H-Bond (Ligand Donor) |
| OAC | NE2 | GLN- 57 | 3.4 | 159.93 | H-Bond (Protein Donor) |
| OAB | NE2 | HIS- 161 | 3.05 | 152.3 | H-Bond (Protein Donor) |
| CAO | CH2 | TRP- 162 | 3.86 | 0 | Hydrophobic |
| OAD | ND2 | ASN- 206 | 3.24 | 157.15 | H-Bond (Protein Donor) |
| NAK | OE2 | GLU- 207 | 3.01 | 0 | Ionic (Ligand Cationic) |
| NAK | OE1 | GLU- 207 | 2.99 | 0 | Ionic (Ligand Cationic) |
| NAK | OE1 | GLU- 207 | 2.99 | 175.59 | H-Bond (Ligand Donor) |
| CAE | CG2 | THR- 210 | 3.52 | 0 | Hydrophobic |
| CAI | CB | ASN- 273 | 4.5 | 0 | Hydrophobic |
| CAI | CD2 | TYR- 345 | 4.28 | 0 | Hydrophobic |
| CAJ | CD2 | TYR- 345 | 4.34 | 0 | Hydrophobic |
| CAP | CZ | TYR- 345 | 4.02 | 0 | Hydrophobic |
| OAD | OE1 | GLU- 416 | 2.98 | 142.72 | H-Bond (Ligand Donor) |
| OAD | OE2 | GLU- 416 | 2.61 | 146.06 | H-Bond (Ligand Donor) |
| CAM | CZ2 | TRP- 465 | 3.68 | 0 | Hydrophobic |
| CAN | CE2 | TRP- 465 | 4.18 | 0 | Hydrophobic |
| OAC | OE1 | GLU- 472 | 3.23 | 165 | H-Bond (Ligand Donor) |
| OAB | NE1 | TRP- 473 | 2.94 | 172.57 | H-Bond (Protein Donor) |
| CAH | CZ | TYR- 481 | 4.18 | 0 | Hydrophobic |
