sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.190 Å
X-ray
2013-08-19
| Name: | Uncharacterized protein |
|---|---|
| ID: | B6YXQ1_THEON |
| AC: | B6YXQ1 |
| Organism: | Thermococcus onnurineus |
| Reign: | Archaea |
| TaxID: | 523850 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 14 % |
| D | 86 % |
| B-Factor: | 48.847 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.866 | 1464.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.40 | 60.60 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 61.93 % |
| 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 |
|---|---|---|
| 36.4341 | 27.9071 | 36.4753 |
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 |
| O1G | NH2 | ARG- 17 | 3.28 | 140.73 | H-Bond (Protein Donor) |
| O1B | NH1 | ARG- 17 | 3.46 | 133.53 | H-Bond (Protein Donor) |
| O2B | NH1 | ARG- 17 | 2.91 | 126.95 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 36 | 4.06 | 0 | Hydrophobic |
| O2B | CZ | ARG- 39 | 3.43 | 0 | Ionic (Protein Cationic) |
| C4' | CB | LEU- 161 | 4.33 | 0 | Hydrophobic |
| C1' | CG | LEU- 161 | 4 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 181 | 2.71 | 135.32 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 181 | 2.9 | 148.13 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 181 | 2.71 | 154.7 | H-Bond (Ligand Donor) |
| N3 | N | LEU- 182 | 3.08 | 150.16 | H-Bond (Protein Donor) |
| N6 | OD1 | ASN- 199 | 3.11 | 168.46 | H-Bond (Ligand Donor) |
| N1 | N | ILE- 200 | 3.14 | 156.06 | H-Bond (Protein Donor) |
