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
2007-12-12
| 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 | 77 % |
| B | 23 % |
| B-Factor: | 28.499 |
|---|---|
| Number of residues: | 45 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.149 | 820.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.98 | 58.02 |
| According to VolSite | |
| HET Code: | ADV |
|---|---|
| Formula: | C16H23N5O13P2 |
| Molecular weight: | 555.327 g/mol |
| DrugBank ID: | DB01975 |
| Buried Surface Area: | 66.98 % |
| Polar Surface area: | 307.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| 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 |
|---|---|---|
| -0.0295278 | 16.5212 | 67.3293 |
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 | 3.47 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 46 | 3.7 | 0 | Aromatic Face/Face |
| C3' | CH2 | TRP- 46 | 3.35 | 0 | Hydrophobic |
| N6 | O | GLU- 47 | 3.08 | 161.09 | H-Bond (Ligand Donor) |
| N1 | N | GLU- 47 | 2.99 | 176.49 | H-Bond (Protein Donor) |
| N7 | NH1 | ARG- 51 | 3.22 | 162 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 84 | 3.83 | 0 | Ionic (Protein Cationic) |
| O1B | NH1 | ARG- 84 | 3.07 | 151.29 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 84 | 3.43 | 172.95 | H-Bond (Protein Donor) |
| CR5 | CB | ALA- 96 | 3.79 | 0 | Hydrophobic |
| C5' | CD1 | LEU- 98 | 4.02 | 0 | Hydrophobic |
| CX | CG | LEU- 98 | 3.57 | 0 | Hydrophobic |
| CR3 | CD2 | LEU- 98 | 4.21 | 0 | Hydrophobic |
| O2A | N | LEU- 98 | 2.84 | 167.71 | H-Bond (Protein Donor) |
| OR1 | N | GLY- 135 | 2.94 | 143.36 | H-Bond (Protein Donor) |
| O3' | OE2 | GLU- 166 | 3.44 | 124 | H-Bond (Ligand Donor) |
| O2B | MG | MG- 301 | 2.2 | 0 | Metal Acceptor |
| O1A | MG | MG- 301 | 2.37 | 0 | Metal Acceptor |
| O1A | MG | MG- 302 | 2.44 | 0 | Metal Acceptor |
| O2A | MG | MG- 303 | 2.34 | 0 | Metal Acceptor |
