sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2013-10-22
| Name: | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic |
|---|---|
| ID: | ISPD_ARATH |
| AC: | P69834 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 2.7.7.60 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 38.867 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.770 | 681.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | PBQ |
|---|---|
| Formula: | C10H4Br5NO |
| Molecular weight: | 553.665 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.68 % |
| Polar Surface area: | 36.01 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 4.78418 | 23.3794 | -20.1662 |
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 |
| BR19 | CG | ARG- 157 | 3.72 | 0 | Hydrophobic |
| BR18 | CB | GLN- 158 | 4.12 | 0 | Hydrophobic |
| BR19 | CB | GLN- 158 | 4.48 | 0 | Hydrophobic |
| BR18 | CG1 | VAL- 161 | 3.71 | 0 | Hydrophobic |
| BR19 | CG2 | VAL- 161 | 4.11 | 0 | Hydrophobic |
| BR13 | CB | ALA- 202 | 3.96 | 0 | Hydrophobic |
| C3 | CB | VAL- 204 | 4.05 | 0 | Hydrophobic |
| BR14 | CG1 | VAL- 204 | 4.34 | 0 | Hydrophobic |
| BR14 | SD | MET- 234 | 4.41 | 0 | Hydrophobic |
| CE2 | CB | GLN- 238 | 3.64 | 0 | Hydrophobic |
| BR13 | CB | ILE- 240 | 4.19 | 0 | Hydrophobic |
| BR17 | CD1 | ILE- 240 | 4.26 | 0 | Hydrophobic |
| BR17 | CD1 | LEU- 245 | 3.56 | 0 | Hydrophobic |
| BR18 | CD1 | LEU- 245 | 4.28 | 0 | Hydrophobic |
| BR18 | CZ | PHE- 249 | 3.76 | 0 | Hydrophobic |
| O | OG | SER- 264 | 2.63 | 120.99 | H-Bond (Protein Donor) |
| CR | CB | SER- 264 | 4.05 | 0 | Hydrophobic |
| BR17 | CB | ILE- 265 | 3.69 | 0 | Hydrophobic |
| BR18 | CG1 | ILE- 265 | 3.71 | 0 | Hydrophobic |
| BR13 | CG1 | VAL- 266 | 4.48 | 0 | Hydrophobic |
| BR17 | CG1 | VAL- 266 | 3.73 | 0 | Hydrophobic |
| CH | CG2 | VAL- 266 | 3.5 | 0 | Hydrophobic |
| CH | CG2 | VAL- 266 | 3.5 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 273 | 4.06 | 0 | Hydrophobic |
