sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2011-01-06
| Name: | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
|---|---|
| ID: | ISPF_BURPS |
| AC: | Q63T71 |
| Organism: | Burkholderia pseudomallei |
| Reign: | Bacteria |
| TaxID: | 272560 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 47 % |
| C | 53 % |
| B-Factor: | 25.256 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.486 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 45.39 | 54.61 |
| According to VolSite | |
| HET Code: | AO9 |
|---|---|
| Formula: | C15H17N6O5S |
| Molecular weight: | 393.398 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.07 % |
| Polar Surface area: | 184.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 36.6147 | -38.3554 | -24.5969 |
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 |
| S37 | CB | HIS- 36 | 3.58 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 36 | 3.84 | 0 | Aromatic Face/Face |
| S37 | CB | SER- 37 | 4.03 | 0 | Hydrophobic |
| O2' | OD1 | ASP- 58 | 3.38 | 132.11 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 58 | 2.72 | 161.75 | H-Bond (Ligand Donor) |
| O3' | OD1 | ASP- 58 | 2.74 | 171.89 | H-Bond (Ligand Donor) |
| S37 | CD1 | ILE- 59 | 3.99 | 0 | Hydrophobic |
| S37 | CD1 | LEU- 78 | 3.69 | 0 | Hydrophobic |
| N4 | O | ALA- 102 | 2.85 | 174.21 | H-Bond (Ligand Donor) |
| N4 | O | PRO- 105 | 2.94 | 163.22 | H-Bond (Ligand Donor) |
| O2 | NZ | LYS- 106 | 2.84 | 137.44 | H-Bond (Protein Donor) |
| O2 | N | LEU- 107 | 3.24 | 126.58 | H-Bond (Protein Donor) |
| N3 | N | LEU- 107 | 2.91 | 174.46 | H-Bond (Protein Donor) |
| O2 | N | ALA- 108 | 2.8 | 136.66 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 133 | 3.97 | 0 | Hydrophobic |
