sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2006-07-20
| Name: | Diphthine synthase |
|---|---|
| ID: | DPHB_PYRHO |
| AC: | O58456 |
| Organism: | Pyrococcus horikoshii |
| Reign: | Archaea |
| TaxID: | 70601 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 98 % |
| B | 2 % |
| B-Factor: | 47.531 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.129 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.00 | 58.00 |
| According to VolSite | |
| HET Code: | SAH |
|---|---|
| Formula: | C14H20N6O5S |
| Molecular weight: | 384.411 g/mol |
| DrugBank ID: | DB01752 |
| Buried Surface Area: | 73.48 % |
| Polar Surface area: | 212.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -14.5622 | -27.9281 | 32.7468 |
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 |
| N6 | O | LEU- 10 | 3.49 | 122.68 | H-Bond (Ligand Donor) |
| C5' | CB | SER- 37 | 4.32 | 0 | Hydrophobic |
| CG | CB | SER- 37 | 3.61 | 0 | Hydrophobic |
| O | N | ASP- 87 | 3.29 | 130.92 | H-Bond (Protein Donor) |
| N | O | VAL- 90 | 2.8 | 172.29 | H-Bond (Ligand Donor) |
| CB | CB | ALA- 91 | 4.33 | 0 | Hydrophobic |
| SD | CB | ALA- 91 | 4.34 | 0 | Hydrophobic |
| O | OG | SER- 115 | 2.75 | 148.85 | H-Bond (Protein Donor) |
| OXT | OG | SER- 115 | 3.17 | 137.18 | H-Bond (Protein Donor) |
| CB | CG2 | ILE- 116 | 4.31 | 0 | Hydrophobic |
| C1' | CG1 | ILE- 116 | 4.33 | 0 | Hydrophobic |
| OXT | N | ILE- 116 | 3.21 | 174.67 | H-Bond (Protein Donor) |
| SD | CD1 | PHE- 165 | 3.97 | 0 | Hydrophobic |
| C4' | CD1 | PHE- 165 | 3.76 | 0 | Hydrophobic |
| O3' | N | LEU- 166 | 2.64 | 135.57 | H-Bond (Protein Donor) |
| N6 | O | ALA- 209 | 2.51 | 158.84 | H-Bond (Ligand Donor) |
| N1 | N | ALA- 209 | 2.77 | 122.8 | H-Bond (Protein Donor) |
| C2' | CB | PRO- 233 | 3.5 | 0 | Hydrophobic |
| O3' | O | HIS- 234 | 3.09 | 158.88 | H-Bond (Ligand Donor) |
| C1' | CG1 | ILE- 235 | 3.97 | 0 | Hydrophobic |
