sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2010-09-02
| Name: | Suppressor of disruption of TFIIS |
|---|---|
| ID: | SDT1_YEAST |
| AC: | P53078 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 16.966 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.580 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 40.43 | 59.57 |
| According to VolSite | |
| HET Code: | U5P |
|---|---|
| Formula: | C9H11N2O9P |
| Molecular weight: | 322.165 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68.92 % |
| Polar Surface area: | 181.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 7.23557 | -4.57214 | -24.766 |
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 |
| O3P | N | ILE- 37 | 2.97 | 150.06 | H-Bond (Protein Donor) |
| C5' | CB | ASP- 38 | 3.55 | 0 | Hydrophobic |
| O3P | N | ASP- 38 | 3.01 | 159.67 | H-Bond (Protein Donor) |
| C2' | SD | MET- 52 | 3.82 | 0 | Hydrophobic |
| C3' | CE | MET- 52 | 4.09 | 0 | Hydrophobic |
| C4' | CD2 | LEU- 84 | 4.33 | 0 | Hydrophobic |
| O2' | OD2 | ASP- 105 | 3.06 | 154.15 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 105 | 2.66 | 177.6 | H-Bond (Ligand Donor) |
| O3P | OG1 | THR- 140 | 2.64 | 170.54 | H-Bond (Protein Donor) |
| O5' | N | ASN- 141 | 3.3 | 129.59 | H-Bond (Protein Donor) |
| O1P | N | ASN- 141 | 3 | 167.38 | H-Bond (Protein Donor) |
| C4' | CB | ASN- 141 | 4.02 | 0 | Hydrophobic |
| C3' | CB | ALA- 142 | 4.14 | 0 | Hydrophobic |
| O1P | NZ | LYS- 177 | 2.51 | 160.4 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 177 | 2.51 | 0 | Ionic (Protein Cationic) |
| O2P | MG | MG- 264 | 2.17 | 0 | Metal Acceptor |
