sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2003-12-01
| Name: | Alpha-2,3-/2,8-sialyltransferase |
|---|---|
| ID: | Q9LAK3_CAMJU |
| AC: | Q9LAK3 |
| Organism: | Campylobacter jejuni |
| Reign: | Bacteria |
| TaxID: | 197 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.116 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.174 | 327.375 |
| % Hydrophobic | % Polar |
|---|---|
| 35.05 | 64.95 |
| According to VolSite | |
| HET Code: | C5P |
|---|---|
| Formula: | C9H12N3O8P |
| Molecular weight: | 321.181 g/mol |
| DrugBank ID: | DB03403 |
| Buried Surface Area: | 74.66 % |
| Polar Surface area: | 190.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 28.6397 | 20.6762 | -7.88276 |
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 |
| C5' | CB | ASN- 9 | 4.06 | 0 | Hydrophobic |
| O4' | N | ASN- 9 | 3.15 | 156.75 | H-Bond (Protein Donor) |
| C4' | SG | CYS- 30 | 4.24 | 0 | Hydrophobic |
| O2P | ND2 | ASN- 31 | 2.79 | 154.66 | H-Bond (Protein Donor) |
| O5' | ND2 | ASN- 31 | 3.3 | 140.16 | H-Bond (Protein Donor) |
| O2' | OG1 | THR- 131 | 2.84 | 149.17 | H-Bond (Ligand Donor) |
| C2' | CB | THR- 131 | 3.45 | 0 | Hydrophobic |
| C3' | CB | SER- 132 | 4.3 | 0 | Hydrophobic |
| O3' | N | SER- 132 | 2.79 | 129.15 | H-Bond (Protein Donor) |
| O2' | N | GLY- 133 | 2.85 | 134.99 | H-Bond (Protein Donor) |
| N3 | N | ASP- 154 | 3.23 | 140.56 | H-Bond (Protein Donor) |
| O2 | N | ASP- 154 | 2.61 | 129.44 | H-Bond (Protein Donor) |
| O2 | N | PHE- 155 | 2.72 | 158.32 | H-Bond (Protein Donor) |
| O3P | OH | TYR- 156 | 2.62 | 149.98 | H-Bond (Protein Donor) |
| N3 | N | TYR- 156 | 3.08 | 170.27 | H-Bond (Protein Donor) |
| C3' | CZ | TYR- 156 | 4.2 | 0 | Hydrophobic |
| C2' | CE1 | TYR- 156 | 4.42 | 0 | Hydrophobic |
| N4 | O | SER- 161 | 2.82 | 147.78 | H-Bond (Ligand Donor) |
| O3P | OH | TYR- 162 | 2.66 | 150.72 | H-Bond (Protein Donor) |
| C5' | CE2 | TYR- 162 | 4.23 | 0 | Hydrophobic |
