sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2014-11-26
| Name: | D-mycarose 3-C-methyltransferase |
|---|---|
| ID: | Q194Q4_STRAA |
| AC: | Q194Q4 |
| Organism: | Streptomyces argillaceus |
| Reign: | Bacteria |
| TaxID: | 41951 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 40.344 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 4 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.675 | 1775.250 |
| % Hydrophobic | % Polar |
|---|---|
| 39.73 | 60.27 |
| According to VolSite | |
| HET Code: | SAM |
|---|---|
| Formula: | C15H23N6O5S |
| Molecular weight: | 399.445 g/mol |
| DrugBank ID: | DB00118 |
| Buried Surface Area: | 63.09 % |
| 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 |
|---|---|---|
| -30.605 | 2.496 | 4.18911 |
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 |
| C2' | CD1 | TYR- 74 | 3.91 | 0 | Hydrophobic |
| SD | CE2 | TYR- 77 | 4.32 | 0 | Hydrophobic |
| C3' | CE2 | TYR- 77 | 4.04 | 0 | Hydrophobic |
| N | O | GLY- 114 | 2.89 | 175.15 | H-Bond (Ligand Donor) |
| CB | CB | ASN- 116 | 3.93 | 0 | Hydrophobic |
| O3' | ND2 | ASN- 116 | 2.85 | 152.65 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 135 | 2.6 | 156.23 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 135 | 2.67 | 154.64 | H-Bond (Ligand Donor) |
| C1' | CG | PRO- 136 | 4.36 | 0 | Hydrophobic |
| N1 | N | PHE- 156 | 3.13 | 161.27 | H-Bond (Protein Donor) |
| N | O | ARG- 177 | 2.81 | 150.59 | H-Bond (Ligand Donor) |
| O | CZ | ARG- 177 | 3.62 | 0 | Ionic (Protein Cationic) |
| CG | CB | HIS- 178 | 4.31 | 0 | Hydrophobic |
| C1' | CG2 | VAL- 179 | 4.18 | 0 | Hydrophobic |
| N | O | HOH- 667 | 3.18 | 153.09 | H-Bond (Ligand Donor) |
