sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2009-06-23
| Name: | Polysialic acid O-acetyltransferase |
|---|---|
| ID: | OATWY_NEIME |
| AC: | Q93S40 |
| Organism: | Neisseria meningitidis |
| Reign: | Bacteria |
| TaxID: | 487 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 60 % |
| C | 40 % |
| B-Factor: | 17.177 |
|---|---|
| Number of residues: | 47 |
| Including | |
| Standard Amino Acids: | 47 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.335 | 695.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.75 | 58.25 |
| According to VolSite | |
| HET Code: | SOP |
|---|---|
| Formula: | C24H36N7O17P3S |
| Molecular weight: | 819.566 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.53 % |
| Polar Surface area: | 429.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 21 |
| X | Y | Z |
|---|---|---|
| 21.0608 | -40.5636 | -13.2041 |
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 |
| CA3 | CG | MET- 108 | 3.75 | 0 | Hydrophobic |
| CA3 | CB | ALA- 110 | 4.34 | 0 | Hydrophobic |
| CP1 | CB | ALA- 110 | 3.45 | 0 | Hydrophobic |
| CPB | CB | ASP- 119 | 4.23 | 0 | Hydrophobic |
| CP4 | CB | ASP- 119 | 4.08 | 0 | Hydrophobic |
| NP2 | OD1 | ASP- 119 | 2.9 | 156.38 | H-Bond (Ligand Donor) |
| NP1 | O | ASP- 119 | 3.2 | 154.55 | H-Bond (Ligand Donor) |
| CP9 | CD1 | ILE- 123 | 4.01 | 0 | Hydrophobic |
| CPB | CD1 | ILE- 123 | 3.87 | 0 | Hydrophobic |
| CPB | CH2 | TRP- 145 | 4.27 | 0 | Hydrophobic |
| CP4 | CZ2 | TRP- 145 | 4.14 | 0 | Hydrophobic |
| S | CZ2 | TRP- 145 | 3.93 | 0 | Hydrophobic |
| OP1 | N | ARG- 148 | 3.15 | 165.65 | H-Bond (Protein Donor) |
| CP1 | CG | ARG- 148 | 3.96 | 0 | Hydrophobic |
| O21 | NZ | LYS- 154 | 3.07 | 177.64 | H-Bond (Protein Donor) |
| O21 | NZ | LYS- 154 | 3.07 | 0 | Ionic (Protein Cationic) |
| CPB | CG1 | VAL- 163 | 4.33 | 0 | Hydrophobic |
| CPA | CG1 | VAL- 163 | 3.74 | 0 | Hydrophobic |
| OP2 | N | SER- 166 | 3.01 | 172.05 | H-Bond (Protein Donor) |
| DuAr | DuAr | TYR- 171 | 3.53 | 0 | Aromatic Face/Face |
| C2' | CD1 | TYR- 171 | 3.94 | 0 | Hydrophobic |
| CPA | CG1 | VAL- 180 | 3.69 | 0 | Hydrophobic |
| C1' | CB | VAL- 189 | 4.29 | 0 | Hydrophobic |
| C4' | CB | VAL- 189 | 3.93 | 0 | Hydrophobic |
| C5' | CG2 | VAL- 189 | 4.13 | 0 | Hydrophobic |
| O22 | NZ | LYS- 190 | 3.19 | 137.09 | H-Bond (Protein Donor) |
| O22 | NZ | LYS- 190 | 3.19 | 0 | Ionic (Protein Cationic) |
