sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.740 Å
X-ray
2000-11-02
| Name: | Modification methylase MboII |
|---|---|
| ID: | MTM2_MORBO |
| AC: | P23192 |
| Organism: | Moraxella bovis |
| Reign: | Bacteria |
| TaxID: | 476 |
| EC Number: | 2.1.1.72 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 27.667 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.546 | 803.250 |
| % Hydrophobic | % Polar |
|---|---|
| 50.42 | 49.58 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 66.81 % |
| Polar Surface area: | 189.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -3.952 | 51.214 | -0.934667 |
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 |
| N1 | N | CYS- 12 | 2.78 | 150.77 | H-Bond (Protein Donor) |
| N | OD1 | ASP- 30 | 2.83 | 151.51 | H-Bond (Ligand Donor) |
| N | OD1 | ASP- 30 | 2.83 | 0 | Ionic (Ligand Cationic) |
| CG | CB | ASP- 30 | 4.38 | 0 | Hydrophobic |
| C3' | CZ2 | TRP- 40 | 4 | 0 | Hydrophobic |
| C2' | CE2 | TRP- 40 | 3.88 | 0 | Hydrophobic |
| CE | CH2 | TRP- 40 | 3.83 | 0 | Hydrophobic |
| O | N | LYS- 197 | 3.1 | 158.46 | H-Bond (Protein Donor) |
| C1' | CD2 | PHE- 220 | 4.05 | 0 | Hydrophobic |
| C5' | CB | PHE- 220 | 3.77 | 0 | Hydrophobic |
| OXT | N | SER- 223 | 2.93 | 162.81 | H-Bond (Protein Donor) |
| OXT | OG | SER- 223 | 2.82 | 163.52 | H-Bond (Protein Donor) |
| O | OG1 | THR- 225 | 2.81 | 162.64 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 241 | 3.5 | 137.37 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 241 | 2.67 | 168.24 | H-Bond (Ligand Donor) |
| O2' | OD1 | ASP- 241 | 2.7 | 156.58 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 241 | 3.47 | 141.61 | H-Bond (Ligand Donor) |
| C1' | CG | MET- 242 | 4.34 | 0 | Hydrophobic |
| N3 | N | MET- 242 | 3.12 | 146.24 | H-Bond (Protein Donor) |
| C3' | CE2 | TYR- 246 | 4.32 | 0 | Hydrophobic |
| N | O | HOH- 526 | 3.11 | 164.12 | H-Bond (Ligand Donor) |
