sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.690 Å
X-ray
2009-07-03
| Name: | 2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase |
|---|---|
| ID: | NCSB1_STRCZ |
| AC: | Q84HC8 |
| Organism: | Streptomyces carzinostaticus |
| Reign: | Bacteria |
| TaxID: | 1897 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 4 % |
| B | 96 % |
| B-Factor: | 66.448 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.393 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.93 | 55.07 |
| According to VolSite | |
| HET Code: | 7NA |
|---|---|
| Formula: | C13H11O4 |
| Molecular weight: | 231.224 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.36 % |
| Polar Surface area: | 69.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -41.8615 | 33.2772 | 6.43665 |
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 |
| O1D | NH2 | ARG- 11 | 3.23 | 132.09 | H-Bond (Protein Donor) |
| O1E | NH2 | ARG- 11 | 3.31 | 163.09 | H-Bond (Protein Donor) |
| C1N | CZ3 | TRP- 96 | 3.31 | 0 | Hydrophobic |
| C1F | CG1 | VAL- 103 | 3.4 | 0 | Hydrophobic |
| C1G | CG2 | VAL- 103 | 3.76 | 0 | Hydrophobic |
| C1B | CE1 | PHE- 146 | 3.88 | 0 | Hydrophobic |
| C1M | SD | MET- 150 | 3.6 | 0 | Hydrophobic |
| C1I | CE | MET- 150 | 3.89 | 0 | Hydrophobic |
| C1L | CE | MET- 150 | 4.01 | 0 | Hydrophobic |
| C1A | CB | ALA- 243 | 3.49 | 0 | Hydrophobic |
| C1Q | SD | MET- 286 | 4.2 | 0 | Hydrophobic |
| C1N | CE | MET- 286 | 3.82 | 0 | Hydrophobic |
| C1N | CD | ARG- 289 | 3.89 | 0 | Hydrophobic |
| C1G | CD | ARG- 289 | 3.34 | 0 | Hydrophobic |
| C1L | CE | MET- 290 | 3.67 | 0 | Hydrophobic |
| C1B | CE2 | TYR- 293 | 3.92 | 0 | Hydrophobic |
| C1B | CZ | PHE- 294 | 3.92 | 0 | Hydrophobic |
