sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2009-04-19
| Name: | Ribonucleoside-diphosphate reductase large subunit |
|---|---|
| ID: | RIR1_HUMAN |
| AC: | P23921 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.17.4.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 70 % |
| B | 30 % |
| B-Factor: | 28.114 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.432 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.57 | 50.43 |
| According to VolSite | |
| HET Code: | DTP |
|---|---|
| Formula: | C10H12N5O12P3 |
| Molecular weight: | 487.150 g/mol |
| DrugBank ID: | DB03222 |
| Buried Surface Area: | 63.87 % |
| Polar Surface area: | 299.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 50.4192 | -0.5133 | 7.35377 |
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 | 2.76 | 166.17 | H-Bond (Ligand Donor) |
| O2A | N | ILE- 228 | 3.08 | 177.3 | H-Bond (Protein Donor) |
| C2' | CD1 | ILE- 228 | 3.78 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 231 | 3.74 | 0 | Hydrophobic |
| O1B | NZ | LYS- 243 | 2.56 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 243 | 3.7 | 0 | Ionic (Protein Cationic) |
| O3A | NZ | LYS- 243 | 3.17 | 164.83 | H-Bond (Protein Donor) |
| O1G | CZ | ARG- 256 | 3.65 | 0 | Ionic (Protein Cationic) |
| O2G | CZ | ARG- 256 | 3.61 | 0 | Ionic (Protein Cationic) |
| O1G | NH1 | ARG- 256 | 2.78 | 175.95 | H-Bond (Protein Donor) |
| O2G | NH2 | ARG- 256 | 2.93 | 135.42 | H-Bond (Protein Donor) |
| C3' | CG | ARG- 256 | 4.49 | 0 | Hydrophobic |
| C4' | CD | ARG- 256 | 3.55 | 0 | Hydrophobic |
| C5' | CG2 | ILE- 262 | 4.28 | 0 | Hydrophobic |
| C4' | CG1 | ILE- 262 | 4.39 | 0 | Hydrophobic |
| C1' | CD1 | ILE- 262 | 4.15 | 0 | Hydrophobic |
| O1G | N | ALA- 263 | 3.3 | 138.77 | H-Bond (Protein Donor) |
| O3B | N | GLY- 264 | 3.09 | 144.16 | H-Bond (Protein Donor) |
| N6 | O | ASP- 287 | 3.01 | 144.3 | H-Bond (Ligand Donor) |
| N1 | N | ASP- 287 | 3.1 | 163.25 | H-Bond (Protein Donor) |
| O2G | MG | MG- 1744 | 2.09 | 0 | Metal Acceptor |
| O2B | MG | MG- 1744 | 1.96 | 0 | Metal Acceptor |
| O1A | MG | MG- 1744 | 1.99 | 0 | Metal Acceptor |
