sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 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 | 33 % |
| B | 20 % |
| C | 47 % |
| B-Factor: | 43.970 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | GTP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.439 | 1977.750 |
| % Hydrophobic | % Polar |
|---|---|
| 36.18 | 63.82 |
| According to VolSite | |
| HET Code: | DTP |
|---|---|
| Formula: | C10H12N5O12P3 |
| Molecular weight: | 487.150 g/mol |
| DrugBank ID: | DB03222 |
| Buried Surface Area: | 73.08 % |
| Polar Surface area: | 299.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 40.3626 | -5.0605 | 3.5158 |
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 | 2.97 | 164.73 | H-Bond (Protein Donor) |
| N3 | ND2 | ASN- 119 | 3.04 | 135.65 | H-Bond (Protein Donor) |
| C1' | CB | ASN- 119 | 3.59 | 0 | Hydrophobic |
| O3' | O | VAL- 156 | 2.73 | 155.94 | H-Bond (Ligand Donor) |
| C2' | CG1 | VAL- 156 | 3.61 | 0 | Hydrophobic |
| C2' | CZ | PHE- 157 | 3.41 | 0 | Hydrophobic |
| C1' | CE1 | PHE- 157 | 3.39 | 0 | Hydrophobic |
| O1A | CZ | ARG- 333 | 3.57 | 0 | Ionic (Protein Cationic) |
| O1A | NH2 | ARG- 333 | 2.67 | 163.87 | H-Bond (Protein Donor) |
| O4' | NH1 | ARG- 333 | 3.02 | 121.63 | H-Bond (Protein Donor) |
| DuAr | CZ | ARG- 333 | 3.81 | 25.52 | Pi/Cation |
| O1G | CZ | ARG- 352 | 3.74 | 0 | Ionic (Protein Cationic) |
| O2G | CZ | ARG- 352 | 3.39 | 0 | Ionic (Protein Cationic) |
| O1G | NH2 | ARG- 352 | 2.67 | 150.57 | H-Bond (Protein Donor) |
| O2G | NH1 | ARG- 352 | 2.8 | 152.82 | H-Bond (Protein Donor) |
| O2G | NH2 | ARG- 352 | 3.14 | 135.28 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 354 | 3.25 | 140.01 | H-Bond (Protein Donor) |
| O3A | NZ | LYS- 354 | 3.49 | 136.56 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 354 | 3.25 | 0 | Ionic (Protein Cationic) |
| N6 | OD1 | ASN- 358 | 3.04 | 149.28 | H-Bond (Ligand Donor) |
| O2A | NE2 | HIS- 376 | 2.64 | 163.02 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 377 | 3.06 | 169.51 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 377 | 3.06 | 0 | Ionic (Protein Cationic) |
| O1G | NZ | LYS- 523 | 3.97 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 523 | 2.85 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 523 | 2.85 | 171.23 | H-Bond (Protein Donor) |
| O1B | O3' | GTP- 704 | 2.88 | 155.33 | H-Bond (Protein Donor) |
| C3' | C1' | GTP- 704 | 4.21 | 0 | Hydrophobic |
| O3G | MG | MG- 704 | 1.9 | 0 | Metal Acceptor |
| O1B | MG | MG- 704 | 2 | 0 | Metal Acceptor |
