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
2011-08-17
| Name: | GDP-fucose protein O-fucosyltransferase 1 |
|---|---|
| ID: | OFUT1_CAEEL |
| AC: | Q18014 |
| Organism: | Caenorhabditis elegans |
| Reign: | Eukaryota |
| TaxID: | 6239 |
| EC Number: | 2.4.1.221 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.834 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.790 | 398.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.47 | 41.53 |
| According to VolSite | |
| HET Code: | GFB |
|---|---|
| Formula: | C16H23N5O15P2 |
| Molecular weight: | 587.326 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 68 % |
| Polar Surface area: | 332.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 7 |
| Rings: | 4 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 10.3479 | 7.29479 | 19.3912 |
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 |
| C5' | CB | ARG- 40 | 4.16 | 0 | Hydrophobic |
| C4' | CD | ARG- 40 | 3.68 | 0 | Hydrophobic |
| C3' | CB | ARG- 40 | 4.3 | 0 | Hydrophobic |
| O4 | NH2 | ARG- 40 | 3.12 | 165.89 | H-Bond (Protein Donor) |
| O3' | N | PHE- 41 | 3.36 | 124.54 | H-Bond (Protein Donor) |
| O1P | N | GLY- 42 | 2.81 | 155.32 | H-Bond (Protein Donor) |
| O3P | N | ASN- 43 | 3.08 | 149.85 | H-Bond (Protein Donor) |
| N7 | NE2 | HIS- 238 | 2.91 | 152.81 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 240 | 3.2 | 158.8 | H-Bond (Protein Donor) |
| O5 | NH2 | ARG- 240 | 3.01 | 132.17 | H-Bond (Protein Donor) |
| O2X | NE | ARG- 240 | 2.84 | 165.56 | H-Bond (Protein Donor) |
| O2X | CZ | ARG- 240 | 3.77 | 0 | Ionic (Protein Cationic) |
| C1 | CZ3 | TRP- 245 | 4.29 | 0 | Hydrophobic |
| C5A | CZ3 | TRP- 245 | 4.48 | 0 | Hydrophobic |
| C6A | CE3 | TRP- 245 | 4.3 | 0 | Hydrophobic |
| C6A | CG2 | VAL- 248 | 3.45 | 0 | Hydrophobic |
| C3 | CE1 | PHE- 261 | 4.01 | 0 | Hydrophobic |
| C5A | CZ | PHE- 261 | 3.76 | 0 | Hydrophobic |
| C1' | CB | ASP- 309 | 4.26 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 334 | 3.32 | 144.06 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 334 | 3.13 | 153.75 | H-Bond (Ligand Donor) |
| C2' | SD | MET- 336 | 3.89 | 0 | Hydrophobic |
| O2X | OG | SER- 355 | 2.59 | 171.34 | H-Bond (Protein Donor) |
| O1X | OG1 | THR- 356 | 2.58 | 175.5 | H-Bond (Protein Donor) |
| O1X | N | THR- 356 | 2.87 | 142.9 | H-Bond (Protein Donor) |
| C3' | CD1 | PHE- 357 | 3.83 | 0 | Hydrophobic |
| C2' | CE1 | PHE- 357 | 4.37 | 0 | Hydrophobic |
