sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.470 Å
X-ray
2012-06-26
| Name: | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD |
|---|---|
| ID: | WBDD2_ECOLX |
| AC: | Q47592 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 562 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.172 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.049 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 55.80 | 44.20 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 72.46 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -11.4468 | 12.9164 | -12.8093 |
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 |
| O3' | O | PRO- 229 | 2.83 | 171.46 | H-Bond (Ligand Donor) |
| C5' | CB | PRO- 229 | 3.8 | 0 | Hydrophobic |
| O1G | NE2 | HIS- 237 | 2.58 | 178.85 | H-Bond (Protein Donor) |
| O2B | NH1 | ARG- 241 | 2.96 | 155.06 | H-Bond (Protein Donor) |
| O2B | OH | TYR- 243 | 2.66 | 156.58 | H-Bond (Protein Donor) |
| C5' | CE1 | TYR- 243 | 3.67 | 0 | Hydrophobic |
| C1' | CE2 | PHE- 245 | 3.92 | 0 | Hydrophobic |
| O1B | NZ | LYS- 252 | 3.9 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 252 | 2.96 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 252 | 2.96 | 133.01 | H-Bond (Protein Donor) |
| N6 | O | GLU- 309 | 3 | 125.17 | H-Bond (Ligand Donor) |
| N1 | N | LEU- 311 | 2.8 | 163.12 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 315 | 3.99 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 368 | 3.57 | 0 | Hydrophobic |
| O2G | MG | MG- 1452 | 2.14 | 0 | Metal Acceptor |
| O1A | MG | MG- 1452 | 1.86 | 0 | Metal Acceptor |
| O3G | MG | MG- 1453 | 1.98 | 0 | Metal Acceptor |
| O1B | MG | MG- 1453 | 2.15 | 0 | Metal Acceptor |
| O2' | O | HOH- 2041 | 2.8 | 137.87 | H-Bond (Protein Donor) |
