sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2011-12-02
| Name: | Orotidine 5'-phosphate decarboxylase |
|---|---|
| ID: | PYRF_VIBCH |
| AC: | Q9KQT7 |
| Organism: | Vibrio cholerae serotype O1 |
| Reign: | Bacteria |
| TaxID: | 243277 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 85 % |
| B | 15 % |
| B-Factor: | 23.101 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.289 | 641.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.63 | 57.37 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -16.3747 | 24.4262 | -18.3707 |
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 |
| C4' | CB | ALA- 9 | 3.55 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 11 | 2.67 | 159.03 | H-Bond (Ligand Donor) |
| O3' | NZ | LYS- 33 | 3.08 | 141.83 | H-Bond (Protein Donor) |
| N3 | OG1 | THR- 120 | 3.38 | 125.31 | H-Bond (Ligand Donor) |
| O4 | OG1 | THR- 120 | 2.61 | 152.53 | H-Bond (Protein Donor) |
| C1' | CB | PRO- 178 | 4.3 | 0 | Hydrophobic |
| O2P | NH1 | ARG- 181 | 3.48 | 130.27 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 181 | 2.81 | 164.62 | H-Bond (Protein Donor) |
| O3P | NH1 | ARG- 181 | 2.98 | 153.11 | H-Bond (Protein Donor) |
| O2P | CZ | ARG- 181 | 3.58 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 181 | 3.82 | 0 | Ionic (Protein Cationic) |
| C4' | CG1 | VAL- 208 | 3.66 | 0 | Hydrophobic |
| O3P | N | GLY- 210 | 2.78 | 165.42 | H-Bond (Protein Donor) |
| O1P | CZ | ARG- 211 | 3.9 | 0 | Ionic (Protein Cationic) |
| O2P | CZ | ARG- 211 | 3.6 | 0 | Ionic (Protein Cationic) |
| O1P | NE | ARG- 211 | 3.04 | 156.61 | H-Bond (Protein Donor) |
| O1P | N | ARG- 211 | 2.87 | 165.89 | H-Bond (Protein Donor) |
| O2P | NH2 | ARG- 211 | 2.79 | 171.72 | H-Bond (Protein Donor) |
| O3P | O | HOH- 267 | 2.78 | 169.41 | H-Bond (Protein Donor) |
