sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2006-05-11
| Name: | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
|---|---|
| ID: | ISPF_ECOLI |
| AC: | P62617 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 4.6.1.12 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 66.505 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.881 | 455.625 |
| % Hydrophobic | % Polar |
|---|---|
| 57.04 | 42.96 |
| According to VolSite | |
| HET Code: | 2AA |
|---|---|
| Formula: | C23H29N5O13P2S |
| Molecular weight: | 677.515 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 38.02 % |
| Polar Surface area: | 293.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 7.83457 | 14.1249 | 32.5963 |
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 |
| C8' | CB | SER- 35 | 3.94 | 0 | Hydrophobic |
| O3 | OD1 | ASP- 56 | 3.33 | 131.66 | H-Bond (Ligand Donor) |
| C1' | CD1 | ILE- 57 | 3.99 | 0 | Hydrophobic |
| O4 | N | GLY- 58 | 3.09 | 126.29 | H-Bond (Protein Donor) |
| C4' | CB | PHE- 61 | 3.57 | 0 | Hydrophobic |
| C13 | CE1 | PHE- 68 | 3.24 | 0 | Hydrophobic |
| C5' | CE2 | PHE- 68 | 3.36 | 0 | Hydrophobic |
| C13 | CB | ALA- 71 | 4.39 | 0 | Hydrophobic |
| C9' | CB | ALA- 71 | 3.68 | 0 | Hydrophobic |
| C9' | CB | SER- 73 | 4.46 | 0 | Hydrophobic |
| C13 | CB | GLU- 75 | 4.32 | 0 | Hydrophobic |
| C12 | CB | GLU- 75 | 4.35 | 0 | Hydrophobic |
| C12 | CB | LEU- 76 | 3.93 | 0 | Hydrophobic |
| C1' | CD2 | LEU- 76 | 4.45 | 0 | Hydrophobic |
| C8' | CD2 | LEU- 76 | 3.73 | 0 | Hydrophobic |
| C10 | CB | LEU- 76 | 3.43 | 0 | Hydrophobic |
| O1' | ZN | ZN- 900 | 2.17 | 0 | Metal Acceptor |
| O4 | O | HOH- 908 | 2.98 | 167.08 | H-Bond (Ligand Donor) |
