sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2014-06-04
| 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 | 47 % |
| C | 23 % |
| D | 30 % |
| B-Factor: | 32.780 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | GTP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.670 | 1721.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.22 | 60.78 |
| According to VolSite | |
| HET Code: | DCP |
|---|---|
| Formula: | C9H12N3O13P3 |
| Molecular weight: | 463.125 g/mol |
| DrugBank ID: | DB03258 |
| Buried Surface Area: | 72.79 % |
| Polar Surface area: | 288.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 15 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 13.3702 | 19.7276 | 5.00079 |
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 |
| O2 | ND2 | ASN- 119 | 2.77 | 148.2 | H-Bond (Protein Donor) |
| O3' | N | ASN- 119 | 2.82 | 168.14 | H-Bond (Protein Donor) |
| C1' | CB | ASN- 119 | 3.6 | 0 | Hydrophobic |
| O3' | O | VAL- 156 | 2.83 | 161.94 | H-Bond (Ligand Donor) |
| C2' | CG1 | VAL- 156 | 3.75 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 157 | 3.48 | 0 | Hydrophobic |
| C2' | CZ | PHE- 157 | 3.37 | 0 | Hydrophobic |
| O4' | NH1 | ARG- 333 | 3.01 | 126.63 | H-Bond (Protein Donor) |
| O2A | NH1 | ARG- 333 | 3.5 | 127.72 | H-Bond (Protein Donor) |
| O2A | NH2 | ARG- 333 | 2.75 | 159.63 | H-Bond (Protein Donor) |
| O2A | CZ | ARG- 333 | 3.57 | 0 | Ionic (Protein Cationic) |
| O1G | NH2 | ARG- 352 | 2.65 | 164.1 | H-Bond (Protein Donor) |
| O3G | NH1 | ARG- 352 | 2.92 | 165.82 | H-Bond (Protein Donor) |
| O1G | CZ | ARG- 352 | 3.63 | 0 | Ionic (Protein Cationic) |
| O3G | CZ | ARG- 352 | 3.65 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 354 | 3.87 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 354 | 2.6 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 354 | 2.6 | 168.5 | H-Bond (Protein Donor) |
| O1A | NE2 | HIS- 376 | 2.66 | 156.52 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 377 | 2.96 | 0 | Ionic (Protein Cationic) |
| O1G | NZ | LYS- 377 | 3.57 | 0 | Ionic (Protein Cationic) |
| O3B | NZ | LYS- 377 | 2.96 | 151.16 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 523 | 3.72 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 523 | 2.93 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 523 | 2.93 | 174.06 | H-Bond (Protein Donor) |
| O1B | MG | MG- 701 | 2.13 | 0 | Metal Acceptor |
| O2G | MG | MG- 701 | 1.91 | 0 | Metal Acceptor |
| C3' | C1' | GTP- 703 | 4.4 | 0 | Hydrophobic |
| C5' | C3' | GTP- 703 | 4.43 | 0 | Hydrophobic |
| O1B | O3' | GTP- 703 | 2.86 | 164.5 | H-Bond (Protein Donor) |
