sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.360 Å
X-ray
2013-06-02
| Name: | Japanin |
|---|---|
| ID: | M1MR49_RHIAP |
| AC: | M1MR49 |
| Organism: | Rhipicephalus appendiculatus |
| Reign: | Eukaryota |
| TaxID: | 34631 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 45.289 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.640 | 1090.125 |
| % Hydrophobic | % Polar |
|---|---|
| 58.20 | 41.80 |
| According to VolSite | |
| HET Code: | CLR |
|---|---|
| Formula: | C27H46O |
| Molecular weight: | 386.654 g/mol |
| DrugBank ID: | DB04540 |
| Buried Surface Area: | 71.84 % |
| Polar Surface area: | 20.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 22.4532 | -61.6361 | 21.225 |
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 |
| C27 | CB | ALA- 6 | 3.71 | 0 | Hydrophobic |
| C26 | CD1 | LEU- 12 | 4.43 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 14 | 4.18 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 14 | 4.41 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 14 | 4.42 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 14 | 4.45 | 0 | Hydrophobic |
| C4 | CB | LEU- 21 | 4.13 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 21 | 4.04 | 0 | Hydrophobic |
| C2 | CB | GLU- 23 | 4.17 | 0 | Hydrophobic |
| C19 | CG | GLU- 23 | 4.46 | 0 | Hydrophobic |
| O1 | N | GLU- 23 | 3.03 | 164.34 | H-Bond (Protein Donor) |
| C2 | CG1 | VAL- 26 | 3.58 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 29 | 3.89 | 0 | Hydrophobic |
| C26 | CG2 | THR- 31 | 3.84 | 0 | Hydrophobic |
| C27 | CD | ARG- 43 | 3.94 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 45 | 4.42 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 45 | 3.96 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 45 | 3.83 | 0 | Hydrophobic |
| C21 | CE1 | PHE- 63 | 4.32 | 0 | Hydrophobic |
| C22 | CE2 | PHE- 63 | 4.21 | 0 | Hydrophobic |
| C23 | CZ | PHE- 63 | 3.88 | 0 | Hydrophobic |
| C24 | CE2 | PHE- 63 | 3.73 | 0 | Hydrophobic |
| C27 | CG1 | VAL- 65 | 4.41 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 74 | 4.28 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 76 | 4.45 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 82 | 4.29 | 0 | Hydrophobic |
| C11 | CB | LEU- 86 | 4.06 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 86 | 4.33 | 0 | Hydrophobic |
| C18 | CB | ALA- 88 | 4.07 | 0 | Hydrophobic |
| C21 | CB | ALA- 88 | 4.15 | 0 | Hydrophobic |
| C22 | CE2 | TYR- 92 | 4.19 | 0 | Hydrophobic |
| C16 | CZ | TYR- 92 | 3.88 | 0 | Hydrophobic |
| C25 | CD1 | LEU- 104 | 4.16 | 0 | Hydrophobic |
| C7 | CB | SER- 115 | 4.06 | 0 | Hydrophobic |
| C15 | CB | SER- 115 | 4.04 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 117 | 4.49 | 0 | Hydrophobic |
| C23 | CZ2 | TRP- 117 | 4.14 | 0 | Hydrophobic |
| C26 | CE2 | TRP- 117 | 3.62 | 0 | Hydrophobic |
| C17 | CZ2 | TRP- 117 | 3.82 | 0 | Hydrophobic |
| O1 | O | HOH- 2014 | 3.29 | 127.92 | H-Bond (Ligand Donor) |
