sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.630 Å
X-ray
2010-04-12
| Name: | Replicase polyprotein 1a |
|---|---|
| ID: | R1A_CVHSA |
| AC: | P0C6U8 |
| Organism: | Human SARS coronavirus |
| Reign: | Viruses |
| TaxID: | 227859 |
| EC Number: | 3.4.22 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 76 % |
| B | 24 % |
| B-Factor: | 41.850 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.952 | 1640.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.88 | 54.12 |
| According to VolSite | |
| HET Code: | GRM |
|---|---|
| Formula: | C26H29N2O3 |
| Molecular weight: | 417.520 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.22 % |
| Polar Surface area: | 52 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -14.3642 | 46.3913 | -40.4571 |
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 |
| C7 | CD2 | LEU- 163 | 4.46 | 0 | Hydrophobic |
| N4 | OD1 | ASP- 165 | 3.43 | 0 | Ionic (Ligand Cationic) |
| C6 | CB | ASP- 165 | 4.43 | 0 | Hydrophobic |
| C8 | CB | ASP- 165 | 3.75 | 0 | Hydrophobic |
| C15 | CG | MET- 209 | 3.74 | 0 | Hydrophobic |
| C21 | CG | PRO- 248 | 4.47 | 0 | Hydrophobic |
| C26 | CG | PRO- 248 | 4.13 | 0 | Hydrophobic |
| C25 | CB | PRO- 248 | 3.59 | 0 | Hydrophobic |
| C28 | CG | PRO- 249 | 3.58 | 0 | Hydrophobic |
| C2 | CB | TYR- 265 | 4.21 | 0 | Hydrophobic |
| C8 | CE1 | TYR- 265 | 4.17 | 0 | Hydrophobic |
| C6 | CE1 | TYR- 269 | 3.33 | 0 | Hydrophobic |
| C29 | CB | TYR- 269 | 4.16 | 0 | Hydrophobic |
| N12 | O | TYR- 269 | 3.13 | 164.8 | H-Bond (Ligand Donor) |
| C21 | CG | GLN- 270 | 3.27 | 0 | Hydrophobic |
| C17 | CB | GLN- 270 | 4.29 | 0 | Hydrophobic |
| C2 | CZ | TYR- 274 | 3.98 | 0 | Hydrophobic |
| C8 | CE2 | TYR- 274 | 4.13 | 0 | Hydrophobic |
| C2 | CG2 | THR- 302 | 3.97 | 0 | Hydrophobic |
