2.400 Å
X-ray
2007-06-07
| Name: | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase |
|---|---|
| ID: | ISPE_AQUAE |
| AC: | O67060 |
| Organism: | Aquifex aeolicus |
| Reign: | Bacteria |
| TaxID: | 224324 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 39.968 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.754 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 40.10 | 59.90 |
| According to VolSite | |

| HET Code: | V12 |
|---|---|
| Formula: | C18H20N6O5 |
| Molecular weight: | 400.389 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.74 % |
| Polar Surface area: | 166.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 16.1204 | -10.7805 | 20.1011 |
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 |
| CBA | CE2 | TYR- 24 | 4 | 0 | Hydrophobic |
| CAZ | CZ | TYR- 24 | 3.74 | 0 | Hydrophobic |
| OAC | ND1 | HIS- 25 | 2.83 | 169.14 | H-Bond (Protein Donor) |
| NAO | N | HIS- 25 | 3.15 | 149.68 | H-Bond (Protein Donor) |
| NAA | O | HIS- 25 | 3.04 | 160.21 | H-Bond (Ligand Donor) |
| NAA | O | LYS- 145 | 3.19 | 163.82 | H-Bond (Ligand Donor) |
| CAH | CB | SER- 170 | 3.74 | 0 | Hydrophobic |
| CB0 | CG2 | THR- 171 | 4.41 | 0 | Hydrophobic |
| CAL | CB | THR- 171 | 3.62 | 0 | Hydrophobic |
| CBC | CD1 | TYR- 175 | 3.53 | 0 | Hydrophobic |