sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.610 Å
X-ray
2013-08-22
| Name: | Ubiquitin-conjugating enzyme E2 R1 |
|---|---|
| ID: | UB2R1_HUMAN |
| AC: | P49427 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 86 % |
| G | 14 % |
| B-Factor: | 55.750 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.946 | 928.125 |
| % Hydrophobic | % Polar |
|---|---|
| 54.18 | 45.82 |
| According to VolSite | |
| HET Code: | U94 |
|---|---|
| Formula: | C20H20Cl2NO6 |
| Molecular weight: | 441.282 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.82 % |
| Polar Surface area: | 118.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 40.3365 | -26.3461 | 29.6302 |
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 |
| CL29 | CE1 | PHE- 28 | 4.03 | 0 | Hydrophobic |
| CL28 | CG2 | ILE- 45 | 3.95 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 45 | 3.89 | 0 | Hydrophobic |
| C22 | CG | PRO- 48 | 3.83 | 0 | Hydrophobic |
| C24 | CG | PRO- 48 | 3.29 | 0 | Hydrophobic |
| C17 | CG | LYS- 48 | 4.2 | 0 | Hydrophobic |
| C17 | CG2 | THR- 51 | 3.53 | 0 | Hydrophobic |
| C3 | CD2 | TYR- 52 | 4.25 | 0 | Hydrophobic |
| C13 | CB | TYR- 52 | 4.16 | 0 | Hydrophobic |
| O12 | N | TYR- 52 | 2.83 | 163.96 | H-Bond (Protein Donor) |
| C13 | CE2 | TYR- 53 | 3.9 | 0 | Hydrophobic |
| CL28 | CD1 | TYR- 53 | 3.96 | 0 | Hydrophobic |
| C20 | CD2 | TYR- 53 | 3.27 | 0 | Hydrophobic |
| C27 | CB | TYR- 53 | 4.1 | 0 | Hydrophobic |
| CL28 | CE2 | PHE- 58 | 3.52 | 0 | Hydrophobic |
| CL29 | CD1 | ILE- 128 | 4.06 | 0 | Hydrophobic |
| CL28 | CD2 | LEU- 131 | 4.24 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 131 | 3.97 | 0 | Hydrophobic |
| C20 | CB | LEU- 131 | 4.19 | 0 | Hydrophobic |
| C16 | CB | ASN- 132 | 4.36 | 0 | Hydrophobic |
| C15 | CE1 | TYR- 148 | 4.14 | 0 | Hydrophobic |
| C3 | CH2 | TRP- 151 | 4.24 | 0 | Hydrophobic |
| C15 | CH2 | TRP- 151 | 3.29 | 0 | Hydrophobic |
| C15 | CE2 | TYR- 161 | 4.28 | 0 | Hydrophobic |
