sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2010-06-07
| Name: | Uncharacterized protein |
|---|---|
| ID: | Q8PC69_XANCP |
| AC: | Q8PC69 |
| Organism: | Xanthomonas campestris pv. campestris |
| Reign: | Bacteria |
| TaxID: | 190485 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 32.183 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.209 | 1049.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.05 | 55.95 |
| According to VolSite | |
| HET Code: | 44P |
|---|---|
| Formula: | C10H13N2O11P2 |
| Molecular weight: | 399.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.98 % |
| Polar Surface area: | 231.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -23.5232 | 10.3922 | 24.6045 |
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 |
| C3A | CG | PRO- 219 | 3.88 | 0 | Hydrophobic |
| C4' | CG | PRO- 219 | 3.87 | 0 | Hydrophobic |
| O2A | ND2 | ASN- 385 | 2.6 | 161.05 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 388 | 3.92 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 388 | 3.41 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 388 | 3.3 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 388 | 3.41 | 156.88 | H-Bond (Protein Donor) |
| O3B | NZ | LYS- 388 | 3.3 | 141.43 | H-Bond (Protein Donor) |
| N3 | O | LEU- 442 | 2.95 | 138.41 | H-Bond (Ligand Donor) |
| O4 | N | LEU- 442 | 3.05 | 176.59 | H-Bond (Protein Donor) |
| O2 | ND1 | HIS- 444 | 3.07 | 150.67 | H-Bond (Protein Donor) |
| C2' | CE2 | TYR- 447 | 4.31 | 0 | Hydrophobic |
| O2B | OH | TYR- 463 | 3.28 | 121.25 | H-Bond (Protein Donor) |
| C3' | CG2 | THR- 467 | 3.76 | 0 | Hydrophobic |
| O3B | OG1 | THR- 467 | 3.46 | 157.78 | H-Bond (Protein Donor) |
| O3B | N | THR- 467 | 3.41 | 157.24 | H-Bond (Protein Donor) |
| O2' | OD2 | ASP- 471 | 2.63 | 165.86 | H-Bond (Ligand Donor) |
