sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 Å
X-ray
2010-09-11
| Name: | Probable tRNA(His) guanylyltransferase |
|---|---|
| ID: | THG1_HUMAN |
| AC: | Q9NWX6 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.7.79 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 9 % |
| B | 91 % |
| B-Factor: | 90.654 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 3 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.702 | 675.000 |
| % Hydrophobic | % Polar |
|---|---|
| 38.00 | 62.00 |
| According to VolSite | |
| HET Code: | DGT |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB02181 |
| Buried Surface Area: | 49.23 % |
| 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 |
|---|---|---|
| -50.4268 | 21.0483 | 35.6291 |
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 |
| O2B | N | PHE- 33 | 2.95 | 120.41 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 33 | 4.13 | 0 | Hydrophobic |
| C1' | CB | PHE- 33 | 4.46 | 0 | Hydrophobic |
| O1B | N | HIS- 34 | 3.45 | 153.51 | H-Bond (Protein Donor) |
| O3' | ND1 | HIS- 34 | 3.43 | 163.4 | H-Bond (Ligand Donor) |
| C2' | CB | HIS- 34 | 4.23 | 0 | Hydrophobic |
| C1' | CB | ALA- 37 | 4.1 | 0 | Hydrophobic |
| N1 | O | ALA- 43 | 3.05 | 169.92 | H-Bond (Ligand Donor) |
| C5' | CB | ASP- 76 | 3.79 | 0 | Hydrophobic |
| O1G | MG | MG- 401 | 2.47 | 0 | Metal Acceptor |
| O2G | MG | MG- 401 | 2.56 | 0 | Metal Acceptor |
| O2B | MG | MG- 401 | 2.28 | 0 | Metal Acceptor |
| O2A | MG | MG- 401 | 2 | 0 | Metal Acceptor |
| O2A | MG | MG- 403 | 2.64 | 0 | Metal Acceptor |
