2.300 Å
X-ray
2005-10-28
| 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: | 38.152 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.313 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 39.10 | 60.90 |
| According to VolSite | |

| HET Code: | GCQ |
|---|---|
| Formula: | C9H10F2N3O10P2 |
| Molecular weight: | 420.134 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 72.22 % |
| Polar Surface area: | 229.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 23.7642 | 53.061 | 16.2359 |
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 |
| O3B | OG | SER- 202 | 2.96 | 157.47 | H-Bond (Protein Donor) |
| O3B | N | SER- 202 | 2.79 | 173.67 | H-Bond (Protein Donor) |
| C4' | CB | SER- 217 | 4.46 | 0 | Hydrophobic |
| C1' | CB | SER- 217 | 4.3 | 0 | Hydrophobic |
| F1 | SG | CYS- 218 | 3.77 | 0 | Hydrophobic |
| O2 | N | GLY- 246 | 2.97 | 126.15 | H-Bond (Protein Donor) |
| F2 | CD | ARG- 293 | 3.64 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 427 | 3.37 | 0 | Hydrophobic |
| C3' | SG | CYS- 428 | 3.43 | 0 | Hydrophobic |
| O1A | N | THR- 608 | 2.58 | 147.34 | H-Bond (Protein Donor) |
| O2A | N | ALA- 609 | 3.07 | 137.06 | H-Bond (Protein Donor) |
| O1B | N | SER- 610 | 3.3 | 131.95 | H-Bond (Protein Donor) |
| O1B | N | THR- 611 | 2.67 | 160.95 | H-Bond (Protein Donor) |
| O1B | OG1 | THR- 611 | 2.7 | 146.86 | H-Bond (Protein Donor) |