sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2002-03-06
| 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: | 13.890 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.733 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 50.48 | 49.52 |
| According to VolSite | |
| HET Code: | NCN |
|---|---|
| Formula: | C11H12NO9P |
| Molecular weight: | 333.188 g/mol |
| DrugBank ID: | DB02382 |
| Buried Surface Area: | 74.85 % |
| Polar Surface area: | 175.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 55.5193 | 39.4642 | 7.94095 |
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 |
| O2' | OE1 | GLU- 174 | 2.74 | 168.24 | H-Bond (Protein Donor) |
| O3' | N | GLY- 176 | 3.18 | 171.02 | H-Bond (Protein Donor) |
| O3P | N | ALA- 178 | 2.53 | 157.1 | H-Bond (Protein Donor) |
| O1P | N | THR- 180 | 3.21 | 153.87 | H-Bond (Protein Donor) |
| O1P | OG1 | THR- 180 | 2.65 | 164.79 | H-Bond (Protein Donor) |
| C5' | CG2 | THR- 180 | 3.6 | 0 | Hydrophobic |
| C5 | CG2 | THR- 180 | 3.83 | 0 | Hydrophobic |
| O2P | N | ALA- 203 | 2.92 | 167.84 | H-Bond (Protein Donor) |
| O5' | N | ALA- 203 | 3.3 | 126.46 | H-Bond (Protein Donor) |
| C4' | CB | ALA- 203 | 4.42 | 0 | Hydrophobic |
| O7 | N | PHE- 265 | 2.99 | 155.15 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 266 | 4.09 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 266 | 3.59 | 0 | Hydrophobic |
| O7 | OG | SER- 291 | 2.6 | 144.49 | H-Bond (Protein Donor) |
| C4 | CB | ARG- 314 | 3.77 | 0 | Hydrophobic |
| O2' | O | LEU- 315 | 3.09 | 158.81 | H-Bond (Ligand Donor) |
| O8 | O | HOH- 1019 | 2.86 | 156.9 | H-Bond (Protein Donor) |
