sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2011-05-27
| Name: | Ribonucleoside-diphosphate reductase large chain 1 |
|---|---|
| ID: | RIR1_YEAST |
| AC: | P21524 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 1.17.4.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 68.300 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.649 | 364.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.63 | 45.37 |
| According to VolSite | |
| HET Code: | DGT |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB02181 |
| Buried Surface Area: | 42.16 % |
| Polar Surface area: | 315.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -10.4026 | 48.3027 | 22.7539 |
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' | OD2 | ASP- 226 | 2.51 | 130.72 | H-Bond (Ligand Donor) |
| O2A | N | ILE- 228 | 3.38 | 162.65 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 228 | 4.44 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 231 | 3.81 | 0 | Hydrophobic |
| O1G | CZ | ARG- 256 | 3.63 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 256 | 3.58 | 0 | Ionic (Protein Cationic) |
| O1G | NH2 | ARG- 256 | 2.75 | 167.13 | H-Bond (Protein Donor) |
| O3G | NH1 | ARG- 256 | 2.7 | 154.82 | H-Bond (Protein Donor) |
| C4' | CD | ARG- 256 | 3.91 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 262 | 3.82 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 262 | 4.07 | 0 | Hydrophobic |
| O3G | N | ALA- 263 | 2.74 | 163.28 | H-Bond (Protein Donor) |
| O3B | N | GLY- 264 | 3.29 | 156.25 | H-Bond (Protein Donor) |
| O1G | MG | MG- 2001 | 1.97 | 0 | Metal Acceptor |
| O1B | MG | MG- 2001 | 2.18 | 0 | Metal Acceptor |
| O1A | MG | MG- 2001 | 2 | 0 | Metal Acceptor |
