sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2013-05-24
| Name: | Nicotinate-nucleotide pyrophosphorylase [carboxylating] |
|---|---|
| ID: | NADC_HUMAN |
| AC: | Q15274 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.4.2.19 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 90 % |
| D | 10 % |
| B-Factor: | 24.413 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.025 | 810.000 |
| % Hydrophobic | % Polar |
|---|---|
| 37.50 | 62.50 |
| According to VolSite | |
| HET Code: | PHT |
|---|---|
| Formula: | C8H4O4 |
| Molecular weight: | 164.115 g/mol |
| DrugBank ID: | DB02746 |
| Buried Surface Area: | 77.41 % |
| Polar Surface area: | 80.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -92.1049 | -0.528417 | -16.2065 |
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 |
| O11 | NH1 | ARG- 102 | 3.11 | 133.27 | H-Bond (Protein Donor) |
| C1 | CB | THR- 137 | 3.69 | 0 | Hydrophobic |
| C6 | CG2 | THR- 137 | 3.82 | 0 | Hydrophobic |
| O8 | NH1 | ARG- 138 | 2.88 | 150.36 | H-Bond (Protein Donor) |
| O12 | N | ARG- 138 | 2.96 | 135.36 | H-Bond (Protein Donor) |
| O8 | CZ | ARG- 138 | 3.99 | 0 | Ionic (Protein Cationic) |
| O8 | CZ | ARG- 161 | 3.82 | 0 | Ionic (Protein Cationic) |
| O9 | CZ | ARG- 161 | 3.88 | 0 | Ionic (Protein Cationic) |
| O8 | NH2 | ARG- 161 | 3.08 | 164.63 | H-Bond (Protein Donor) |
| O9 | NE | ARG- 161 | 2.97 | 168.18 | H-Bond (Protein Donor) |
| C4 | CE | MET- 169 | 3.37 | 0 | Hydrophobic |
| O8 | NZ | LYS- 171 | 2.71 | 159.51 | H-Bond (Protein Donor) |
| O11 | NZ | LYS- 171 | 2.64 | 131.48 | H-Bond (Protein Donor) |
| O8 | NZ | LYS- 171 | 2.71 | 0 | Ionic (Protein Cationic) |
| O11 | NZ | LYS- 171 | 2.64 | 0 | Ionic (Protein Cationic) |
| C5 | CD1 | LEU- 220 | 4.04 | 0 | Hydrophobic |
| C6 | CB | SER- 268 | 4.29 | 0 | Hydrophobic |
