sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2016-03-22
| Name: | NADH pyrophosphatase |
|---|---|
| ID: | D6JHV3_ECOLX |
| AC: | D6JHV3 |
| Organism: | Escherichia coli B354 |
| Reign: | Bacteria |
| TaxID: | 550677 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 88 % |
| B | 12 % |
| B-Factor: | 43.312 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.537 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.60 | 54.40 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.13 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 16.4656 | -5.25482 | -26.9901 |
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 |
| DuAr | DuAr | TYR- 124 | 3.75 | 0 | Aromatic Face/Face |
| C2B | CZ | TYR- 124 | 3.88 | 0 | Hydrophobic |
| C4D | SG | CYS- 130 | 3.74 | 0 | Hydrophobic |
| C4N | CD1 | ILE- 132 | 3.73 | 0 | Hydrophobic |
| C5N | CB | ALA- 158 | 4.28 | 0 | Hydrophobic |
| C1B | CD2 | PHE- 160 | 4.14 | 0 | Hydrophobic |
| C5D | CE2 | PHE- 160 | 3.61 | 0 | Hydrophobic |
| C5B | CE2 | PHE- 160 | 3.82 | 0 | Hydrophobic |
| C4D | CZ | PHE- 160 | 3.77 | 0 | Hydrophobic |
| N7N | OE1 | GLN- 192 | 3.16 | 152.1 | H-Bond (Ligand Donor) |
| O3D | OG | SER- 199 | 3.46 | 159.12 | H-Bond (Ligand Donor) |
| C3N | CE | MET- 201 | 4.1 | 0 | Hydrophobic |
| O7N | N | ALA- 241 | 3.47 | 151.95 | H-Bond (Protein Donor) |
| C4N | CB | ALA- 241 | 4.43 | 0 | Hydrophobic |
