sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2003-11-06
| Name: | ADP-ribosylation factor 1 | ARF guanine-nucleotide exchange factor 1 |
|---|---|---|
| ID: | ARF1_HUMAN | GEA1_YEAST |
| AC: | P84077 | P47102 |
| Organism: | Homo sapiens | Saccharomyces cerevisiae |
| Reign: | Eukaryota | |
| TaxID: | 9606 | 559292 |
| EC Number: | / | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 64 % |
| B | 36 % |
| B-Factor: | 31.863 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.774 | 894.375 |
| % Hydrophobic | % Polar |
|---|---|
| 44.53 | 55.47 |
| According to VolSite | |
| HET Code: | AFB |
|---|---|
| Formula: | C16H24O4 |
| Molecular weight: | 280.359 g/mol |
| DrugBank ID: | DB07348 |
| Buried Surface Area: | 74.2 % |
| 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 |
|---|---|---|
| 42.0091 | 7.37985 | 38.4866 |
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 |
| C12 | CD1 | PHE- 51 | 4.44 | 0 | Hydrophobic |
| C8 | CE2 | PHE- 51 | 4.15 | 0 | Hydrophobic |
| C6 | CD2 | PHE- 51 | 3.74 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 53 | 4.44 | 0 | Hydrophobic |
| C9 | CH2 | TRP- 66 | 3.75 | 0 | Hydrophobic |
| C4 | CE3 | TRP- 66 | 3.71 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 66 | 4.18 | 0 | Hydrophobic |
| C6 | CB | ASP- 67 | 4.39 | 0 | Hydrophobic |
| OC4 | N | ASP- 67 | 3.16 | 170.14 | H-Bond (Protein Donor) |
| OC7 | NE1 | TRP- 78 | 3.08 | 138.92 | H-Bond (Protein Donor) |
| C7 | CE2 | TRP- 78 | 4.45 | 0 | Hydrophobic |
| C12 | CZ | TYR- 81 | 4.24 | 0 | Hydrophobic |
| C14 | CE2 | TYR- 81 | 3.54 | 0 | Hydrophobic |
| C6 | CB | SER- 198 | 3.71 | 0 | Hydrophobic |
| OC7 | OH | TYR- 256 | 2.73 | 146.35 | H-Bond (Protein Donor) |
| C8 | CE2 | TYR- 256 | 3.85 | 0 | Hydrophobic |
| C8 | SD | MET- 260 | 4 | 0 | Hydrophobic |
| C9 | CE | MET- 260 | 4.4 | 0 | Hydrophobic |
| C12 | CG | MET- 260 | 4.01 | 0 | Hydrophobic |
| C12 | CB | THR- 263 | 4.38 | 0 | Hydrophobic |
| C13 | CG2 | THR- 263 | 3.65 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 270 | 4.22 | 0 | Hydrophobic |
| OC1 | O | HOH- 713 | 2.78 | 179.96 | H-Bond (Protein Donor) |
