sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 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 |
|---|---|
| A | 26 % |
| B | 29 % |
| D | 45 % |
| B-Factor: | 40.154 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 2 |
| Cofactors: | GTP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.287 | 2419.875 |
| % Hydrophobic | % Polar |
|---|---|
| 38.91 | 61.09 |
| According to VolSite | |
| HET Code: | DGT |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB02181 |
| Buried Surface Area: | 75 % |
| 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 |
|---|---|---|
| 0.460419 | -11.6215 | -3.52887 |
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' | N | ASN- 119 | 2.96 | 166.67 | H-Bond (Protein Donor) |
| C1' | CB | ASN- 119 | 3.6 | 0 | Hydrophobic |
| O3' | O | VAL- 156 | 2.66 | 154.86 | H-Bond (Ligand Donor) |
| C2' | CG1 | VAL- 156 | 3.59 | 0 | Hydrophobic |
| C2' | CZ | PHE- 157 | 3.51 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 157 | 3.46 | 0 | Hydrophobic |
| O1A | NH2 | ARG- 333 | 2.74 | 160.79 | H-Bond (Protein Donor) |
| O4' | NH1 | ARG- 333 | 3.22 | 131.22 | H-Bond (Protein Donor) |
| O1A | CZ | ARG- 333 | 3.67 | 0 | Ionic (Protein Cationic) |
| DuAr | CZ | ARG- 333 | 3.63 | 18.05 | Pi/Cation |
| O2G | NH2 | ARG- 352 | 2.94 | 145.68 | H-Bond (Protein Donor) |
| O3G | NH2 | ARG- 352 | 3.12 | 138.68 | H-Bond (Protein Donor) |
| O3G | NH1 | ARG- 352 | 2.93 | 147.5 | H-Bond (Protein Donor) |
| O3G | CZ | ARG- 352 | 3.44 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 354 | 3.55 | 0 | Ionic (Protein Cationic) |
| O6 | ND2 | ASN- 358 | 3.03 | 162.23 | H-Bond (Protein Donor) |
| O6 | NE | ARG- 372 | 3.23 | 120.29 | H-Bond (Protein Donor) |
| O2A | NE2 | HIS- 376 | 2.6 | 163.99 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 377 | 3.54 | 0 | Ionic (Protein Cationic) |
| O1B | NZ | LYS- 377 | 2.57 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 377 | 3.88 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 377 | 2.92 | 147.83 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 377 | 2.57 | 124.07 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 523 | 3.05 | 154.24 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 523 | 3.05 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 523 | 3.69 | 0 | Ionic (Protein Cationic) |
| O2B | MG | MG- 703 | 1.9 | 0 | Metal Acceptor |
| O2B | O3' | GTP- 704 | 2.7 | 148.42 | H-Bond (Protein Donor) |
| O3A | O3' | GTP- 704 | 3.4 | 135.56 | H-Bond (Protein Donor) |
| C5' | C3' | GTP- 704 | 4.4 | 0 | Hydrophobic |
| C3' | C1' | GTP- 704 | 4.18 | 0 | Hydrophobic |
