sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.910 Å
X-ray
2011-03-30
| Name: | Sugar 3-ketoreductase |
|---|---|
| ID: | B3TMR8_9ACTN |
| AC: | B3TMR8 |
| Organism: | Actinomadura kijaniata |
| Reign: | Bacteria |
| TaxID: | 46161 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.549 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.385 | 273.375 |
| % Hydrophobic | % Polar |
|---|---|
| 59.26 | 40.74 |
| According to VolSite | |
| HET Code: | TLO |
|---|---|
| Formula: | C16H18N2O11P2 |
| Molecular weight: | 476.268 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 46.12 % |
| Polar Surface area: | 206.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -43.4014 | -13.2617 | -18.2543 |
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 |
| CD2 | CD1 | ILE- 20 | 3.33 | 0 | Hydrophobic |
| O2B | CZ | ARG- 23 | 3.41 | 0 | Ionic (Protein Cationic) |
| O2B | NH1 | ARG- 23 | 3.05 | 137.14 | H-Bond (Protein Donor) |
| O2B | NH2 | ARG- 23 | 2.95 | 141.31 | H-Bond (Protein Donor) |
| O1B | NE | ARG- 24 | 2.91 | 148.75 | H-Bond (Protein Donor) |
| O1B | NH2 | ARG- 24 | 2.91 | 144.99 | H-Bond (Protein Donor) |
| O1B | CZ | ARG- 24 | 3.34 | 0 | Ionic (Protein Cationic) |
| C4' | CG2 | ILE- 161 | 3.66 | 0 | Hydrophobic |
| C1' | CD2 | TYR- 240 | 3.81 | 0 | Hydrophobic |
| C5M | CZ | TYR- 240 | 3.64 | 0 | Hydrophobic |
| C5' | CE2 | TYR- 240 | 4.2 | 0 | Hydrophobic |
| O2A | OH | TYR- 240 | 2.59 | 165.51 | H-Bond (Protein Donor) |
| O2A | OG1 | THR- 260 | 2.6 | 165 | H-Bond (Protein Donor) |
| CD1 | CG2 | THR- 260 | 3.91 | 0 | Hydrophobic |
