sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.940 Å
X-ray
2008-05-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.160 | 5.360 | 5.260 | 0.220 | 5.660 | 3 |
| Name: | UDP-N-acetylmuramoylalanine--D-glutamate ligase |
|---|---|
| ID: | MURD_ECOLI |
| AC: | P14900 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 6.3.2.9 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.816 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.067 | 1505.250 |
| % Hydrophobic | % Polar |
|---|---|
| 35.65 | 64.35 |
| According to VolSite | |
| HET Code: | LKM |
|---|---|
| Formula: | C23H17FN2O7S |
| Molecular weight: | 484.454 g/mol |
| DrugBank ID: | DB08112 |
| Buried Surface Area: | 55.02 % |
| Polar Surface area: | 167.83 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 1.60132 | -20.5055 | -20.2292 |
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 |
| N31 | N | THR- 36 | 3.48 | 162.79 | H-Bond (Protein Donor) |
| C26 | CB | THR- 36 | 4.4 | 0 | Hydrophobic |
| C26 | CG | ARG- 37 | 4.11 | 0 | Hydrophobic |
| F2 | CG | ARG- 37 | 3.44 | 0 | Hydrophobic |
| C25 | CD | ARG- 37 | 3.72 | 0 | Hydrophobic |
| DuAr | CZ | ARG- 37 | 3.68 | 160.54 | Pi/Cation |
| CG | CG2 | THR- 321 | 4.36 | 0 | Hydrophobic |
| O | NZ | LYS- 348 | 3.72 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 348 | 2.88 | 0 | Ionic (Protein Cationic) |
| OXT | NZ | LYS- 348 | 2.88 | 157.81 | H-Bond (Protein Donor) |
| CG | CB | ALA- 414 | 3.84 | 0 | Hydrophobic |
| OE2 | OG | SER- 415 | 2.71 | 169.29 | H-Bond (Protein Donor) |
| OE2 | N | SER- 415 | 2.84 | 158.11 | H-Bond (Protein Donor) |
| CG | CG | LEU- 416 | 4.05 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 416 | 3.57 | 0 | Hydrophobic |
| OE1 | N | PHE- 422 | 2.91 | 150.91 | H-Bond (Protein Donor) |
| O | O | HOH- 2136 | 2.65 | 158.2 | H-Bond (Protein Donor) |
