sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 Å
X-ray
2008-10-10
| Name: | Bifunctional protein GlmU |
|---|---|
| ID: | GLMU_HAEIN |
| AC: | P43889 |
| Organism: | Haemophilus influenzae |
| Reign: | Bacteria |
| TaxID: | 71421 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 32.877 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.493 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 36.09 | 63.91 |
| According to VolSite | |
| HET Code: | LZR |
|---|---|
| Formula: | C25H26N4O4 |
| Molecular weight: | 446.498 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.93 % |
| Polar Surface area: | 83.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 6 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 81.3815 | 35.2329 | 37.4806 |
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 | LEU- 11 | 4.27 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 11 | 3.51 | 0 | Hydrophobic |
| C18 | CB | ALA- 13 | 3.91 | 0 | Hydrophobic |
| C17 | CD | LYS- 25 | 4 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 26 | 3.53 | 0 | Hydrophobic |
| C21 | CG2 | THR- 82 | 4.26 | 0 | Hydrophobic |
| C5 | CG2 | THR- 82 | 4.07 | 0 | Hydrophobic |
| C21 | CB | ALA- 85 | 4.07 | 0 | Hydrophobic |
| C15 | CD1 | TYR- 103 | 4.13 | 0 | Hydrophobic |
| C16 | CB | TYR- 103 | 3.64 | 0 | Hydrophobic |
| C1 | CB | TYR- 103 | 4.15 | 0 | Hydrophobic |
| N3 | OD1 | ASP- 105 | 2.9 | 147.24 | H-Bond (Ligand Donor) |
| C17 | CB | ASP- 105 | 4.18 | 0 | Hydrophobic |
| C16 | CB | ALA- 106 | 4.07 | 0 | Hydrophobic |
| C30 | CE2 | TYR- 139 | 3.47 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 223 | 4.15 | 0 | Hydrophobic |
| O29 | N | GLY- 225 | 3.02 | 150.94 | H-Bond (Protein Donor) |
