sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 Å
X-ray
2006-08-01
| Name: | Deoxyribodipyrimidine photo-lyase |
|---|---|
| ID: | PHR_THET8 |
| AC: | P61497 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | 4.1.99.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.832 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.221 | 1326.375 |
| % Hydrophobic | % Polar |
|---|---|
| 43.00 | 57.00 |
| According to VolSite | |
| HET Code: | HDF |
|---|---|
| Formula: | C16H17N3O7 |
| Molecular weight: | 363.322 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.5 % |
| Polar Surface area: | 162.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 44.8507 | 11.6933 | 32.0201 |
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 |
| C3' | CB | ARG- 9 | 4.02 | 0 | Hydrophobic |
| N3 | O | VAL- 34 | 2.8 | 164.93 | H-Bond (Ligand Donor) |
| O4 | N | ASP- 36 | 2.97 | 167.11 | H-Bond (Protein Donor) |
| C5A | CB | ASN- 39 | 3.75 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 40 | 4.19 | 0 | Hydrophobic |
| C7 | CB | ARG- 46 | 4.44 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 50 | 3.87 | 0 | Hydrophobic |
| C5A | CD1 | PHE- 50 | 3.41 | 0 | Hydrophobic |
| C6 | CB | PHE- 50 | 3.43 | 0 | Hydrophobic |
| C5' | CB | SER- 96 | 4.19 | 0 | Hydrophobic |
| O5' | OG | SER- 96 | 3.48 | 137.35 | H-Bond (Protein Donor) |
| O5' | OG | SER- 96 | 3.48 | 136.42 | H-Bond (Ligand Donor) |
| O3' | NH1 | ARG- 104 | 2.94 | 138.91 | H-Bond (Protein Donor) |
| O5' | NH2 | ARG- 104 | 2.96 | 159.26 | H-Bond (Protein Donor) |
| O5' | NH1 | ARG- 104 | 3.31 | 138.03 | H-Bond (Protein Donor) |
| C9 | CD2 | LEU- 218 | 3.54 | 0 | Hydrophobic |
| O2 | O | HOH- 2003 | 2.8 | 154.88 | H-Bond (Protein Donor) |
