sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.390 Å
X-ray
2013-05-24
| Name: | tRNA(His) guanylyltransferase {ECO:0000256|PIRNR:PIRNR028980} |
|---|---|
| ID: | Q5AFK5_CANAL |
| AC: | Q5AFK5 |
| Organism: | Candida albicans |
| Reign: | Eukaryota |
| TaxID: | 237561 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 94 % |
| D | 6 % |
| B-Factor: | 39.655 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 4 |
| Water Molecules: | 0 |
| Cofactors: | ATP |
| Metals: | MG MG MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.315 | 2281.500 |
| % Hydrophobic | % Polar |
|---|---|
| 30.47 | 69.53 |
| According to VolSite | |
| HET Code: | ATP |
|---|---|
| Formula: | C10H12N5O13P3 |
| Molecular weight: | 503.149 g/mol |
| DrugBank ID: | DB00171 |
| Buried Surface Area: | 54.47 % |
| Polar Surface area: | 319.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 17 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 14.8564 | 52.2175 | -6.43916 |
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 |
| O3G | N | GLY- 32 | 2.79 | 176.55 | H-Bond (Protein Donor) |
| O1B | N | PHE- 33 | 2.91 | 157.78 | H-Bond (Protein Donor) |
| C5' | CB | PHE- 33 | 3.97 | 0 | Hydrophobic |
| O2B | N | HIS- 34 | 3.05 | 163.17 | H-Bond (Protein Donor) |
| O2B | ND1 | HIS- 34 | 2.98 | 120.94 | H-Bond (Protein Donor) |
| C1' | CB | SER- 37 | 4.13 | 0 | Hydrophobic |
| N3 | NZ | LYS- 44 | 3.12 | 168.29 | H-Bond (Protein Donor) |
| N6 | O | ASP- 47 | 3.24 | 164.28 | H-Bond (Ligand Donor) |
| N1 | N | ASP- 47 | 2.74 | 151.3 | H-Bond (Protein Donor) |
| C5' | CB | ASP- 76 | 4.45 | 0 | Hydrophobic |
| O2A | MG | MG- 403 | 2.26 | 0 | Metal Acceptor |
| O2G | MG | MG- 404 | 2.06 | 0 | Metal Acceptor |
| O1B | MG | MG- 404 | 2.04 | 0 | Metal Acceptor |
| O2A | MG | MG- 404 | 2.13 | 0 | Metal Acceptor |
