sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
2003-10-28
| Name: | Cytohesin-2 | ADP-ribosylation factor 1 |
|---|---|---|
| ID: | CYH2_HUMAN | ARF1_BOVIN |
| AC: | Q99418 | P84080 |
| Organism: | Homo sapiens | Bos taurus |
| Reign: | Eukaryota | |
| TaxID: | 9606 | 9913 |
| EC Number: | / | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 62 % |
| F | 38 % |
| B-Factor: | 22.823 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.771 | 1356.750 |
| % Hydrophobic | % Polar |
|---|---|
| 38.56 | 61.44 |
| According to VolSite | |
| HET Code: | AFB |
|---|---|
| Formula: | C16H24O4 |
| Molecular weight: | 280.359 g/mol |
| DrugBank ID: | DB07348 |
| Buried Surface Area: | 74.98 % |
| Polar Surface area: | 66.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -20.5651 | -2.30475 | 20.8921 |
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 |
| C8 | CE1 | PHE- 51 | 4.05 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 51 | 3.83 | 0 | Hydrophobic |
| C9 | CH2 | TRP- 66 | 3.87 | 0 | Hydrophobic |
| C4 | CD2 | TRP- 66 | 3.67 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 66 | 4.07 | 0 | Hydrophobic |
| C6 | CB | ASP- 67 | 4.24 | 0 | Hydrophobic |
| C4 | CB | ASP- 67 | 4.47 | 0 | Hydrophobic |
| OC4 | N | ASP- 67 | 2.86 | 171.58 | H-Bond (Protein Donor) |
| OC7 | NE1 | TRP- 78 | 3.06 | 134.19 | H-Bond (Protein Donor) |
| C7 | CE2 | TRP- 78 | 3.99 | 0 | Hydrophobic |
| C12 | CZ | TYR- 81 | 4.2 | 0 | Hydrophobic |
| C14 | CE1 | TYR- 81 | 3.51 | 0 | Hydrophobic |
| C6 | CB | ALA- 157 | 3.97 | 0 | Hydrophobic |
| OC7 | OH | TYR- 190 | 2.62 | 174.76 | H-Bond (Protein Donor) |
| C8 | CE2 | TYR- 190 | 4.03 | 0 | Hydrophobic |
| C8 | CG | MET- 194 | 3.82 | 0 | Hydrophobic |
| C9 | CE | MET- 194 | 4.4 | 0 | Hydrophobic |
| C12 | CB | MET- 194 | 4.08 | 0 | Hydrophobic |
| C12 | CB | THR- 197 | 4.23 | 0 | Hydrophobic |
| C13 | CG2 | THR- 197 | 3.73 | 0 | Hydrophobic |
| C13 | CB | ASP- 198 | 4.28 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 204 | 3.76 | 0 | Hydrophobic |
| OC7 | O | HOH- 406 | 2.69 | 160.68 | H-Bond (Ligand Donor) |
| OC1 | O | HOH- 422 | 3.44 | 161.19 | H-Bond (Protein Donor) |
