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
2011-03-16
| 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: | 40.968 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.195 | 425.250 |
| % Hydrophobic | % Polar |
|---|---|
| 67.46 | 32.54 |
| According to VolSite | |
| HET Code: | 30A |
|---|---|
| Formula: | C14H9ClN3O3 |
| Molecular weight: | 302.693 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 85.75 % |
| Polar Surface area: | 90.55 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 16.155 | 57.6941 | -19.7752 |
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 |
| O4 | CZ | ARG- 157 | 3.93 | 0 | Ionic (Protein Cationic) |
| O4 | NH1 | ARG- 157 | 2.86 | 155 | H-Bond (Protein Donor) |
| CL | CG1 | ILE- 177 | 4.07 | 0 | Hydrophobic |
| C12 | CB | ALA- 202 | 4.38 | 0 | Hydrophobic |
| C13 | CB | VAL- 204 | 3.75 | 0 | Hydrophobic |
| CL | CB | GLN- 238 | 4.31 | 0 | Hydrophobic |
| C12 | CB | GLN- 238 | 3.6 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 240 | 4.4 | 0 | Hydrophobic |
| C11 | CB | ILE- 240 | 3.95 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 245 | 4.44 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 263 | 3.76 | 0 | Hydrophobic |
| C15 | CB | VAL- 263 | 3.77 | 0 | Hydrophobic |
| N19 | N | ILE- 265 | 2.99 | 151.06 | H-Bond (Protein Donor) |
| O7 | N | VAL- 266 | 2.93 | 151.41 | H-Bond (Protein Donor) |
| C14 | CG2 | VAL- 266 | 3.57 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 266 | 3.62 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 273 | 3.6 | 0 | Hydrophobic |
