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
2011-02-26
| Name: | Orotidine-5-phosphate decarboxylase/orotate phosphoribosyltransferase, putative |
|---|---|
| ID: | E9BCQ9_LEIDB |
| AC: | E9BCQ9 |
| Organism: | Leishmania donovani |
| Reign: | Eukaryota |
| TaxID: | 981087 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 82.050 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.729 | 958.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.35 | 49.65 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.59 % |
| 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 |
|---|---|---|
| 0.774524 | -15.6124 | 29.6009 |
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 |
| O4' | NZ | LYS- 279 | 3.25 | 152.73 | H-Bond (Protein Donor) |
| N3 | O | ILE- 288 | 2.88 | 158.87 | H-Bond (Ligand Donor) |
| O4 | N | ILE- 288 | 3.44 | 169.29 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 291 | 3.29 | 147 | H-Bond (Protein Donor) |
| O3' | OD2 | ASP- 371 | 3.02 | 174.6 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 371 | 3.25 | 121.07 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 372 | 3.02 | 147.2 | H-Bond (Ligand Donor) |
| C2' | CD1 | LEU- 373 | 4.25 | 0 | Hydrophobic |
| O2P | N | SER- 375 | 2.8 | 141.13 | H-Bond (Protein Donor) |
| O2P | OG | SER- 375 | 2.88 | 153.8 | H-Bond (Protein Donor) |
| O2P | N | THR- 376 | 2.83 | 130.64 | H-Bond (Protein Donor) |
| O2P | N | GLY- 377 | 3.12 | 122.1 | H-Bond (Protein Donor) |
| O3P | N | GLY- 377 | 3.35 | 134.43 | H-Bond (Protein Donor) |
| O3P | N | THR- 379 | 2.62 | 168.49 | H-Bond (Protein Donor) |
| C5' | CB | THR- 379 | 3.84 | 0 | Hydrophobic |
| O4 | NE | ARG- 403 | 2.94 | 166.71 | H-Bond (Protein Donor) |
