sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-03-05
| Name: | Cyclic dipeptide N-prenyltransferase |
|---|---|
| ID: | D1D8L6_ASPFM |
| AC: | D1D8L6 |
| Organism: | Neosartorya fumigata |
| Reign: | Eukaryota |
| TaxID: | 746128 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 65.962 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.098 | 1535.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.38 | 44.62 |
| According to VolSite | |
| HET Code: | 0MV |
|---|---|
| Formula: | C18H15N3O2 |
| Molecular weight: | 305.331 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.14 % |
| Polar Surface area: | 73.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -31.188 | -16.9408 | -27.0093 |
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 |
| CAD | SG | CYS- 107 | 3.91 | 0 | Hydrophobic |
| CAH | CG | LEU- 109 | 4.32 | 0 | Hydrophobic |
| CE2 | CD2 | LEU- 109 | 3.71 | 0 | Hydrophobic |
| CZ2 | CD2 | LEU- 109 | 3.7 | 0 | Hydrophobic |
| NE1 | OE2 | GLU- 116 | 2.82 | 163.52 | H-Bond (Ligand Donor) |
| CH2 | CB | ALA- 131 | 3.93 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 201 | 3.66 | 0 | Hydrophobic |
| CAC | CG2 | THR- 203 | 3.58 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 206 | 4.14 | 0 | Hydrophobic |
| CH2 | CG1 | VAL- 206 | 4.14 | 0 | Hydrophobic |
| CAG | CE1 | PHE- 223 | 3.45 | 0 | Hydrophobic |
| CB | SD | MET- 349 | 4.04 | 0 | Hydrophobic |
