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
1995-12-16
| Name: | ADP-ribosylation factor 1 |
|---|---|
| ID: | ARF1_RAT |
| AC: | P84079 |
| Organism: | Rattus norvegicus |
| Reign: | Eukaryota |
| TaxID: | 10116 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 19 % |
| B | 81 % |
| B-Factor: | 30.163 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.243 | 934.875 |
| % Hydrophobic | % Polar |
|---|---|
| 22.02 | 77.98 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 67.5 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -16.1573 | -7.00768 | 26.075 |
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 |
| O3B | N | ALA- 27 | 2.66 | 157.02 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 27 | 4.27 | 0 | Hydrophobic |
| O1B | N | GLY- 29 | 3.15 | 164.91 | H-Bond (Protein Donor) |
| O3A | N | GLY- 29 | 3.24 | 121.16 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 30 | 2.63 | 168.45 | H-Bond (Protein Donor) |
| O1B | N | LYS- 30 | 3.07 | 150.89 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 30 | 2.63 | 0 | Ionic (Protein Cationic) |
| O2B | N | THR- 31 | 3.13 | 149.26 | H-Bond (Protein Donor) |
| O1A | N | THR- 32 | 2.8 | 134.24 | H-Bond (Protein Donor) |
| O1A | OG1 | THR- 32 | 2.53 | 159.88 | H-Bond (Protein Donor) |
| N7 | ND2 | ASN- 126 | 2.96 | 148.41 | H-Bond (Protein Donor) |
| O4' | NZ | LYS- 127 | 3.2 | 139.04 | H-Bond (Protein Donor) |
| O6 | N | LYS- 127 | 3.42 | 126.74 | H-Bond (Protein Donor) |
| N1 | OD1 | ASP- 129 | 2.84 | 168.83 | H-Bond (Ligand Donor) |
| C2' | CG2 | THR- 161 | 4.49 | 0 | Hydrophobic |
| O2B | MG | MG- 182 | 2.34 | 0 | Metal Acceptor |
