sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.270 Å
X-ray
2014-06-05
| Name: | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 |
|---|---|
| ID: | SAMH1_HUMAN |
| AC: | Q9Y3Z3 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.1.5 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 49.363 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.130 | 725.625 |
| % Hydrophobic | % Polar |
|---|---|
| 34.42 | 65.58 |
| According to VolSite | |
| HET Code: | DGT |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB02181 |
| Buried Surface Area: | 65.2 % |
| Polar Surface area: | 315.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 35.1495 | -2.14732 | -32.1935 |
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 |
| O3' | NE2 | GLN- 149 | 2.88 | 165.91 | H-Bond (Protein Donor) |
| C2' | CD2 | LEU- 150 | 3.66 | 0 | Hydrophobic |
| O1A | NH1 | ARG- 164 | 3.08 | 166.78 | H-Bond (Protein Donor) |
| O4' | NH2 | ARG- 164 | 3.26 | 153.3 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 206 | 3.32 | 140.37 | H-Bond (Protein Donor) |
| O2A | NE2 | HIS- 210 | 3.49 | 127.47 | H-Bond (Protein Donor) |
| O2A | NE2 | HIS- 215 | 2.56 | 142.15 | H-Bond (Protein Donor) |
| O5' | NE2 | HIS- 215 | 3.23 | 133.96 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 312 | 3.76 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 312 | 2.92 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 312 | 2.92 | 151.03 | H-Bond (Protein Donor) |
| O1G | OH | TYR- 315 | 2.55 | 155.54 | H-Bond (Protein Donor) |
| C5' | CE2 | TYR- 315 | 3.25 | 0 | Hydrophobic |
| C4' | CD2 | TYR- 315 | 3.98 | 0 | Hydrophobic |
| C3' | CD1 | TYR- 315 | 3.63 | 0 | Hydrophobic |
| O3' | OD2 | ASP- 319 | 2.7 | 154.25 | H-Bond (Ligand Donor) |
| O1G | NE | ARG- 366 | 2.89 | 176.96 | H-Bond (Protein Donor) |
| O1G | NH2 | ARG- 366 | 3.5 | 134.7 | H-Bond (Protein Donor) |
| O2G | NH2 | ARG- 366 | 3.24 | 155.69 | H-Bond (Protein Donor) |
| O1G | CZ | ARG- 366 | 3.66 | 0 | Ionic (Protein Cationic) |
| C3' | CZ | TYR- 374 | 4.07 | 0 | Hydrophobic |
| C2' | CE1 | TYR- 374 | 3.54 | 0 | Hydrophobic |
| O6 | NE2 | GLN- 375 | 2.86 | 130.62 | H-Bond (Protein Donor) |
| O3G | MG | MG- 702 | 2.55 | 0 | Metal Acceptor |
| O1B | MG | MG- 702 | 1.84 | 0 | Metal Acceptor |
