sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-12-05
| Name: | Nicotinate-nucleotide pyrophosphorylase [carboxylating] |
|---|---|
| ID: | I3LK75_PIG |
| AC: | I3LK75 |
| Organism: | Sus scrofa |
| Reign: | Eukaryota |
| TaxID: | 9823 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 6 % |
| B | 94 % |
| B-Factor: | 37.604 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.171 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 37.45 | 62.55 |
| According to VolSite | |
| HET Code: | NCN |
|---|---|
| Formula: | C11H12NO9P |
| Molecular weight: | 333.188 g/mol |
| DrugBank ID: | DB02382 |
| Buried Surface Area: | 65.24 % |
| 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 |
|---|---|---|
| -17.3981 | 93.9901 | 16.4789 |
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 |
| C5 | CB | THR- 137 | 4.05 | 0 | Hydrophobic |
| C3 | CB | ARG- 138 | 4.36 | 0 | Hydrophobic |
| O8 | CZ | ARG- 138 | 3.79 | 0 | Ionic (Protein Cationic) |
| O8 | NH1 | ARG- 138 | 2.78 | 156.28 | H-Bond (Protein Donor) |
| O2P | NZ | LYS- 139 | 3.46 | 0 | Ionic (Protein Cationic) |
| O7 | CZ | ARG- 161 | 3.31 | 0 | Ionic (Protein Cationic) |
| O8 | CZ | ARG- 161 | 3.53 | 0 | Ionic (Protein Cationic) |
| O7 | NH2 | ARG- 161 | 2.83 | 141.41 | H-Bond (Protein Donor) |
| O7 | NE | ARG- 161 | 3 | 135.99 | H-Bond (Protein Donor) |
| C2' | CE | LYS- 171 | 4.05 | 0 | Hydrophobic |
| O3' | OE1 | GLU- 201 | 2.54 | 144.01 | H-Bond (Ligand Donor) |
| C2' | CD2 | LEU- 220 | 3.84 | 0 | Hydrophobic |
| C3' | CB | SER- 248 | 4.38 | 0 | Hydrophobic |
