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
2006-06-28
| Name: | ADP-sugar pyrophosphatase |
|---|---|
| ID: | NUDT5_HUMAN |
| AC: | Q9UKK9 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.6.1.13 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 74 % |
| B | 26 % |
| B-Factor: | 35.521 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.152 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.09 | 58.91 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.75 % |
| Polar Surface area: | 316.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -0.0179167 | 16.3115 | 67.8881 |
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 |
| C1' | CH2 | TRP- 28 | 3.41 | 0 | Hydrophobic |
| C2' | CZ3 | TRP- 46 | 3.62 | 0 | Hydrophobic |
| C3' | CH2 | TRP- 46 | 3.52 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 46 | 3.66 | 0 | Aromatic Face/Face |
| N1 | N | GLU- 47 | 2.81 | 171.64 | H-Bond (Protein Donor) |
| N6 | O | GLU- 47 | 2.99 | 163.38 | H-Bond (Ligand Donor) |
| N7 | NH1 | ARG- 51 | 3 | 157.32 | H-Bond (Protein Donor) |
| O2D | NH2 | ARG- 51 | 3.37 | 138.09 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 84 | 3.95 | 0 | Ionic (Protein Cationic) |
| O2B | CZ | ARG- 84 | 3.71 | 0 | Ionic (Protein Cationic) |
| O1B | NH1 | ARG- 84 | 2.99 | 161.91 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 84 | 2.98 | 165.41 | H-Bond (Protein Donor) |
| C4D | CB | ALA- 96 | 4.03 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 98 | 3.96 | 0 | Hydrophobic |
| C5D | CD2 | LEU- 98 | 4.12 | 0 | Hydrophobic |
| O2A | N | LEU- 98 | 3.02 | 162.99 | H-Bond (Protein Donor) |
| O3D | OD1 | ASP- 133 | 3.15 | 162.78 | H-Bond (Ligand Donor) |
| C1D | CG | PRO- 134 | 4.45 | 0 | Hydrophobic |
| O2D | N | GLY- 135 | 3.05 | 125.41 | H-Bond (Protein Donor) |
| O1A | MG | MG- 302 | 2.42 | 0 | Metal Acceptor |
| O2B | MG | MG- 302 | 2.51 | 0 | Metal Acceptor |
| O3D | O | HOH- 484 | 2.73 | 144.8 | H-Bond (Protein Donor) |
| O2A | O | HOH- 487 | 2.98 | 179.98 | H-Bond (Protein Donor) |
