sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2014-12-09
| Name: | Mycinamicin III 3''-O-methyltransferase |
|---|---|
| ID: | MYCF_MICGR |
| AC: | Q49492 |
| Organism: | Micromonospora griseorubida |
| Reign: | Bacteria |
| TaxID: | 28040 |
| EC Number: | 2.1.1.237 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 20.671 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.036 | 843.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.80 | 49.20 |
| According to VolSite | |
| HET Code: | MVI |
|---|---|
| Formula: | C35H58NO11 |
| Molecular weight: | 668.835 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 37.64 % |
| Polar Surface area: | 165.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 26.4683 | 29.7824 | 97.7243 |
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 |
| CAA | CB | ALA- 30 | 3.79 | 0 | Hydrophobic |
| CAV | CE1 | TYR- 49 | 3.91 | 0 | Hydrophobic |
| CAA | CZ | TYR- 49 | 3.85 | 0 | Hydrophobic |
| CBN | SD | MET- 56 | 3.67 | 0 | Hydrophobic |
| CAD | CG | MET- 132 | 4.07 | 0 | Hydrophobic |
| CBK | CD2 | LEU- 134 | 4.03 | 0 | Hydrophobic |
| CAA | CD1 | TYR- 137 | 3.65 | 0 | Hydrophobic |
| CAU | CG | TYR- 137 | 3.45 | 0 | Hydrophobic |
| CBP | CD2 | TYR- 137 | 4.18 | 0 | Hydrophobic |
| CAA | CG1 | VAL- 141 | 4.34 | 0 | Hydrophobic |
| OAL | OD1 | ASP- 191 | 2.6 | 164 | H-Bond (Ligand Donor) |
| CAF | SG | CYS- 219 | 3.9 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 220 | 3.87 | 0 | Hydrophobic |
| OAK | OE1 | GLN- 246 | 2.62 | 142.38 | H-Bond (Ligand Donor) |
| OAK | MG | MG- 302 | 2.12 | 0 | Metal Acceptor |
| OAL | MG | MG- 302 | 1.82 | 0 | Metal Acceptor |
| OAK | O | HOH- 483 | 3.04 | 146.93 | H-Bond (Protein Donor) |
