sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2001-06-28
| Name: | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase |
|---|---|
| ID: | COBT_SALTY |
| AC: | Q05603 |
| Organism: | Salmonella typhimurium |
| Reign: | Bacteria |
| TaxID: | 99287 |
| EC Number: | 2.4.2.21 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.028 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.157 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | PMO |
|---|---|
| Formula: | C13H15N2O8P |
| Molecular weight: | 358.241 g/mol |
| DrugBank ID: | DB04176 |
| Buried Surface Area: | 64.47 % |
| Polar Surface area: | 158.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 58.1191 | 40.6446 | 10.7927 |
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 |
| C11 | CG1 | VAL- 84 | 3.82 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 84 | 3.73 | 0 | Hydrophobic |
| C4 | CG | GLN- 88 | 4.13 | 0 | Hydrophobic |
| O2' | OE1 | GLU- 174 | 2.54 | 167.31 | H-Bond (Ligand Donor) |
| C7A | CD1 | LEU- 175 | 4.48 | 0 | Hydrophobic |
| O3' | N | GLY- 176 | 3 | 161.71 | H-Bond (Protein Donor) |
| C7A | CE | MET- 177 | 4.15 | 0 | Hydrophobic |
| C3' | CE | MET- 177 | 4.37 | 0 | Hydrophobic |
| C7 | SD | MET- 177 | 3.8 | 0 | Hydrophobic |
| O3P | N | ALA- 178 | 2.66 | 166.08 | H-Bond (Protein Donor) |
| O1P | N | THR- 180 | 3.1 | 153.89 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 180 | 2.57 | 164.83 | H-Bond (Protein Donor) |
| C5' | CG2 | THR- 180 | 3.45 | 0 | Hydrophobic |
| C7 | CB | ALA- 203 | 4.16 | 0 | Hydrophobic |
| C4' | CB | ALA- 203 | 4.43 | 0 | Hydrophobic |
| O2P | N | ALA- 203 | 2.92 | 170.35 | H-Bond (Protein Donor) |
| O5' | N | ALA- 203 | 3.37 | 125.03 | H-Bond (Protein Donor) |
| O2P | O | HOH- 1007 | 2.73 | 159.43 | H-Bond (Protein Donor) |
| O2P | O | HOH- 1014 | 2.66 | 179.96 | H-Bond (Protein Donor) |
| O3P | O | HOH- 1025 | 2.63 | 167.88 | H-Bond (Protein Donor) |
