sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
1997-07-21
| Name: | Ribonucleoside-diphosphate reductase 1 subunit alpha |
|---|---|
| ID: | RIR1_ECOLI |
| AC: | P00452 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 1.17.4.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 71.910 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.310 | 540.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 47.47 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -40.2097 | 111.421 | 38.1571 |
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 |
| O2B | NZ | LYS- 9 | 3.09 | 153.3 | H-Bond (Protein Donor) |
| O2A | NZ | LYS- 9 | 2.65 | 146.17 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 9 | 3.09 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 9 | 3.53 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 9 | 2.65 | 0 | Ionic (Protein Cationic) |
| N6 | OE2 | GLU- 15 | 3.19 | 130.92 | H-Bond (Ligand Donor) |
| N6 | O | ARG- 16 | 3.17 | 154.37 | H-Bond (Ligand Donor) |
| N1 | N | ASN- 18 | 2.74 | 144.9 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 21 | 2.57 | 124.93 | H-Bond (Protein Donor) |
| O3G | NZ | LYS- 21 | 3.33 | 156.53 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 21 | 2.57 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 21 | 3.33 | 0 | Ionic (Protein Cationic) |
| C1' | CG1 | ILE- 22 | 4.31 | 0 | Hydrophobic |
| C3' | CG2 | VAL- 25 | 3.92 | 0 | Hydrophobic |
| O2A | OG1 | THR- 55 | 3.09 | 158.08 | H-Bond (Protein Donor) |
| C5' | CE1 | PHE- 87 | 4.42 | 0 | Hydrophobic |
| O1B | NZ | LYS- 91 | 2.98 | 147.61 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 91 | 2.98 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 91 | 3.51 | 0 | Ionic (Protein Cationic) |
