sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2009-10-23
| Name: | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase |
|---|---|
| ID: | ISPF_BURP1 |
| AC: | Q3JRA0 |
| Organism: | Burkholderia pseudomallei |
| Reign: | Bacteria |
| TaxID: | 320372 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 43 % |
| B | 57 % |
| B-Factor: | 23.447 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.451 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 48.03 | 51.97 |
| According to VolSite | |
| HET Code: | 829 |
|---|---|
| Formula: | C15H17N5O5 |
| Molecular weight: | 347.326 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.41 % |
| Polar Surface area: | 150.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 9.68604 | -27.06 | -21.5274 |
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 |
| O2' | OD1 | ASP- 58 | 2.76 | 157.35 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 58 | 3.14 | 122.79 | H-Bond (Ligand Donor) |
| C08 | CG2 | ILE- 59 | 4.22 | 0 | Hydrophobic |
| O3' | N | GLY- 60 | 3.13 | 122.51 | H-Bond (Protein Donor) |
| N4 | O | ALA- 102 | 2.76 | 174.23 | H-Bond (Ligand Donor) |
| N4 | O | PRO- 105 | 3.04 | 156.59 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 107 | 3.17 | 135.09 | H-Bond (Protein Donor) |
| N3 | N | LEU- 107 | 2.93 | 164.16 | H-Bond (Protein Donor) |
| O2 | N | ALA- 108 | 2.91 | 157.69 | H-Bond (Protein Donor) |
| C2' | CB | ALA- 133 | 4.17 | 0 | Hydrophobic |
| C12 | CD | LYS- 134 | 3.8 | 0 | Hydrophobic |
| O15 | N | THR- 135 | 2.93 | 164.06 | H-Bond (Protein Donor) |
| N10 | ZN | ZN- 163 | 2.15 | 0 | Metal Acceptor |
| DuAr | ZN | ZN- 163 | 3.51 | 95.48 | Pi/Cation |
| O3' | O | HOH- 197 | 2.68 | 160.63 | H-Bond (Ligand Donor) |
