sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2012-06-15
| Name: | Protease Do-like 2, chloroplastic |
|---|---|
| ID: | DEGP2_ARATH |
| AC: | O82261 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 3.4.21 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 72.848 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.214 | 874.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.88 | 52.12 |
| According to VolSite | |
| HET Code: | UNK_UNK_TRP_UNK |
|---|---|
| Formula: | C20H28N5O4 |
| Molecular weight: | 402.467 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 40.07 % |
| Polar Surface area: | 147.79 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 5 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 18.0595 | -1.38769 | 36.5709 |
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 |
| O | N | LEU- 323 | 3.01 | 133.33 | H-Bond (Protein Donor) |
| O | N | GLY- 324 | 3.28 | 156.57 | H-Bond (Protein Donor) |
| N | O | VAL- 325 | 2.89 | 157.57 | H-Bond (Ligand Donor) |
| CB | CG1 | VAL- 325 | 4.21 | 0 | Hydrophobic |
| CB | CD2 | LEU- 326 | 3.99 | 0 | Hydrophobic |
| CE2 | CG | LEU- 326 | 3.62 | 0 | Hydrophobic |
| CH2 | CB | LEU- 326 | 4.12 | 0 | Hydrophobic |
| N | O | LEU- 327 | 3.02 | 136.39 | H-Bond (Ligand Donor) |
| O | N | LEU- 327 | 2.76 | 150.33 | H-Bond (Protein Donor) |
| CB | CD1 | LEU- 327 | 3.72 | 0 | Hydrophobic |
| CH2 | CB | ARG- 351 | 4.35 | 0 | Hydrophobic |
| CZ3 | CG | GLU- 353 | 3.56 | 0 | Hydrophobic |
| CB | CD2 | PHE- 392 | 4.12 | 0 | Hydrophobic |
| CB | CG | ARG- 393 | 3.93 | 0 | Hydrophobic |
| CB | CD1 | ILE- 396 | 3.84 | 0 | Hydrophobic |
| CZ2 | CG1 | VAL- 476 | 4.43 | 0 | Hydrophobic |
