sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2013-10-03
| Name: | 7,8-dihydro-8-oxoguanine triphosphatase |
|---|---|
| ID: | 8ODP_HUMAN |
| AC: | P36639 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.6.1.55 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.834 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.680 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.98 | 47.02 |
| According to VolSite | |
| HET Code: | VGH |
|---|---|
| Formula: | C21H23Cl2FN5O |
| Molecular weight: | 451.345 g/mol |
| DrugBank ID: | DB08865 |
| Buried Surface Area: | 59.19 % |
| Polar Surface area: | 82.57 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -16.6097 | -14.96 | 11.0316 |
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 |
| F | CB | TYR- 7 | 3.31 | 0 | Hydrophobic |
| CL2 | CD2 | LEU- 9 | 3.93 | 0 | Hydrophobic |
| CL | CB | PHE- 27 | 4.23 | 0 | Hydrophobic |
| O27 | ND2 | ASN- 33 | 2.76 | 139.47 | H-Bond (Protein Donor) |
| CL2 | CE2 | PHE- 72 | 4.49 | 0 | Hydrophobic |
| C20 | CZ | PHE- 74 | 3.76 | 0 | Hydrophobic |
| F | SD | MET- 81 | 4.37 | 0 | Hydrophobic |
| C18 | CE | MET- 81 | 3.78 | 0 | Hydrophobic |
| C2 | CE | MET- 81 | 3.8 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 83 | 4.25 | 0 | Hydrophobic |
| F | CG1 | VAL- 83 | 3.91 | 0 | Hydrophobic |
| CL2 | CG1 | VAL- 83 | 4.07 | 0 | Hydrophobic |
| CL | CZ2 | TRP- 117 | 4.36 | 0 | Hydrophobic |
| C1 | CE2 | TRP- 117 | 3.44 | 0 | Hydrophobic |
| C15 | CB | TRP- 117 | 4.1 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 117 | 3.88 | 0 | Aromatic Edge/Face |
| DuAr | DuAr | TRP- 117 | 3.75 | 0 | Aromatic Face/Face |
| N22 | OD2 | ASP- 119 | 3 | 152.79 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 119 | 3.41 | 124.97 | H-Bond (Ligand Donor) |
| N23 | OD1 | ASP- 119 | 2.63 | 167.78 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 120 | 3.31 | 121.15 | H-Bond (Ligand Donor) |
| N22 | O | HOH- 2031 | 2.76 | 130.92 | H-Bond (Ligand Donor) |
