sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.780 Å
X-ray
2006-08-07
| Name: | Rac-like GTP-binding protein ARAC7 |
|---|---|
| ID: | RAC7_ARATH |
| AC: | O82480 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 15 % |
| D | 85 % |
| B-Factor: | 14.865 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.906 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.79 | 41.21 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 73.83 % |
| 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 |
|---|---|---|
| 58.3267 | 12.5458 | 121.83 |
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 |
| O2B | N | ALA- 16 | 2.73 | 146.77 | H-Bond (Protein Donor) |
| C5' | CB | ALA- 16 | 4.24 | 0 | Hydrophobic |
| O1B | N | GLY- 18 | 2.89 | 150.38 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 19 | 2.99 | 164.37 | H-Bond (Protein Donor) |
| O1B | N | LYS- 19 | 2.82 | 162.38 | H-Bond (Protein Donor) |
| O1B | NZ | LYS- 19 | 2.99 | 0 | Ionic (Protein Cationic) |
| O2B | NZ | LYS- 19 | 3.95 | 0 | Ionic (Protein Cationic) |
| O3B | N | THR- 20 | 3 | 163.91 | H-Bond (Protein Donor) |
| O1A | N | CYS- 21 | 2.75 | 158.39 | H-Bond (Protein Donor) |
| C2' | SG | CYS- 21 | 3.86 | 0 | Hydrophobic |
| C2' | CZ | PHE- 31 | 4.3 | 0 | Hydrophobic |
| C2' | CD1 | ILE- 36 | 3.68 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 121 | 2.75 | 161.47 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 121 | 2.88 | 170.29 | H-Bond (Ligand Donor) |
| N2 | OD2 | ASP- 125 | 3.1 | 166.94 | H-Bond (Ligand Donor) |
| N2 | OD1 | ASP- 125 | 3.38 | 138.36 | H-Bond (Ligand Donor) |
| C4' | CB | ALA- 130 | 4.38 | 0 | Hydrophobic |
| O6 | N | LYS- 159 | 3.38 | 157.06 | H-Bond (Protein Donor) |
| O3B | MG | MG- 1181 | 2.03 | 0 | Metal Acceptor |
