sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2004-07-06
| Name: | Probable ADP-ribose 1''-phosphate phosphatase YML087W |
|---|---|
| ID: | YMX7_YEAST |
| AC: | Q04299 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | 3.1.3.84 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.698 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | NA |
| Ligandability | Volume (Å3) |
|---|---|
| 0.629 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 48.57 | 51.43 |
| According to VolSite | |
| HET Code: | APR |
|---|---|
| Formula: | C15H21N5O14P2 |
| Molecular weight: | 557.300 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 77.26 % |
| 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 |
|---|---|---|
| 46.7206 | 2.3375 | 17.2929 |
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 |
| O2' | OD2 | ASP- 23 | 2.96 | 161.85 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 23 | 3.27 | 130.24 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 23 | 2.61 | 169.57 | H-Bond (Ligand Donor) |
| N3 | N | THR- 24 | 3.37 | 139 | H-Bond (Protein Donor) |
| N1 | N | LEU- 54 | 3.05 | 147.76 | H-Bond (Protein Donor) |
| N6 | OE1 | GLN- 55 | 2.97 | 170.58 | H-Bond (Ligand Donor) |
| C5' | CG | PRO- 78 | 4 | 0 | Hydrophobic |
| C5D | CB | PRO- 78 | 4.39 | 0 | Hydrophobic |
| O2D | ND2 | ASN- 80 | 3.08 | 134 | H-Bond (Protein Donor) |
| O3D | ND2 | ASN- 80 | 3.33 | 147.42 | H-Bond (Protein Donor) |
| C3D | CB | ASN- 80 | 4.14 | 0 | Hydrophobic |
| O1A | N | PHE- 89 | 2.69 | 164.76 | H-Bond (Protein Donor) |
| O2D | OD2 | ASP- 90 | 2.99 | 164.04 | H-Bond (Ligand Donor) |
| C3D | CG2 | VAL- 149 | 3.81 | 0 | Hydrophobic |
| C4' | CB | PRO- 191 | 4.4 | 0 | Hydrophobic |
| O1B | N | CYS- 194 | 3.24 | 123.18 | H-Bond (Protein Donor) |
| C3' | CB | THR- 195 | 4.29 | 0 | Hydrophobic |
| O3' | OG1 | THR- 195 | 2.62 | 154.9 | H-Bond (Protein Donor) |
| O2B | N | GLY- 196 | 2.81 | 137.71 | H-Bond (Protein Donor) |
| O2A | N | TYR- 197 | 3.02 | 166.37 | H-Bond (Protein Donor) |
| C1D | CD1 | TYR- 197 | 3.73 | 0 | Hydrophobic |
| C4D | CB | TYR- 197 | 4.01 | 0 | Hydrophobic |
| O2B | N | ALA- 198 | 2.83 | 172.59 | H-Bond (Protein Donor) |
| O3' | O | HOH- 300 | 2.89 | 179.97 | H-Bond (Protein Donor) |
