sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.590 Å
X-ray
2014-04-25
| 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 | 58 % |
| B | 42 % |
| B-Factor: | 41.989 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.446 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.57 | 49.43 |
| According to VolSite | |
| HET Code: | GTP |
|---|---|
| Formula: | C10H12N5O14P3 |
| Molecular weight: | 519.149 g/mol |
| DrugBank ID: | DB04137 |
| Buried Surface Area: | 58.49 % |
| Polar Surface area: | 335.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -7.19837 | -6.72069 | -16.4316 |
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 |
| O2A | NZ | LYS- 116 | 3.47 | 0 | Ionic (Protein Cationic) |
| O5' | NZ | LYS- 116 | 3.02 | 125.36 | H-Bond (Protein Donor) |
| O3' | NZ | LYS- 116 | 3.38 | 134.92 | H-Bond (Protein Donor) |
| C2' | CG | LYS- 116 | 4.32 | 0 | Hydrophobic |
| O3' | O | VAL- 117 | 3.32 | 158.46 | H-Bond (Ligand Donor) |
| C2' | CD1 | ILE- 118 | 3.37 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 137 | 2.76 | 157.31 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 137 | 3.09 | 163.56 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 137 | 3.23 | 132.89 | H-Bond (Ligand Donor) |
| O6 | NE2 | GLN- 142 | 3.23 | 144.24 | H-Bond (Protein Donor) |
| O6 | NH1 | ARG- 145 | 3.43 | 123.28 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 156 | 4.13 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 156 | 4.15 | 0 | Hydrophobic |
| C1' | CG1 | VAL- 156 | 4.42 | 0 | Hydrophobic |
| C5' | CG1 | VAL- 378 | 3.52 | 0 | Hydrophobic |
| O1A | CZ | ARG- 451 | 2.92 | 0 | Ionic (Protein Cationic) |
| O2G | N | LEU- 453 | 3.24 | 139.24 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 455 | 2.98 | 163.43 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 455 | 2.98 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 455 | 3.89 | 0 | Ionic (Protein Cationic) |
