sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2011-12-06
| Name: | Probable NDP-rhamnosyltransferase |
|---|---|
| ID: | Q9ALM8_9PSEU |
| AC: | Q9ALM8 |
| Organism: | Saccharopolyspora spinosa |
| Reign: | Bacteria |
| TaxID: | 60894 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.664 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.293 | 1431.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.01 | 45.99 |
| According to VolSite | |
| HET Code: | 0CX |
|---|---|
| Formula: | C24H34O5 |
| Molecular weight: | 402.524 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 48.84 % |
| Polar Surface area: | 83.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -0.691 | 60.39 | -18.4872 |
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 |
| C23 | CD2 | LEU- 8 | 3.85 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 8 | 3.92 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 8 | 3.46 | 0 | Hydrophobic |
| C23 | CG | PRO- 9 | 3.68 | 0 | Hydrophobic |
| C12 | CE2 | TYR- 10 | 3.44 | 0 | Hydrophobic |
| O2 | NE2 | HIS- 13 | 2.86 | 164.84 | H-Bond (Protein Donor) |
| C3 | CG2 | THR- 90 | 3.39 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 93 | 3.23 | 164.33 | H-Bond (Protein Donor) |
| C18 | CB | ASN- 93 | 3.76 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 94 | 4.39 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 94 | 4.24 | 0 | Hydrophobic |
| C2 | CB | VAL- 94 | 4.4 | 0 | Hydrophobic |
| C22 | CB | SER- 97 | 4.43 | 0 | Hydrophobic |
| C8 | CZ2 | TRP- 142 | 4.35 | 0 | Hydrophobic |
| C9 | CE | MET- 227 | 4.46 | 0 | Hydrophobic |
| C24 | CZ | PHE- 315 | 4.42 | 0 | Hydrophobic |
| C11 | CE1 | PHE- 315 | 3.75 | 0 | Hydrophobic |
| C3 | CZ | PHE- 315 | 4.41 | 0 | Hydrophobic |
| C9 | CD1 | PHE- 315 | 3.61 | 0 | Hydrophobic |
| C8 | CG | PHE- 315 | 3.62 | 0 | Hydrophobic |
