sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2005-08-08
| Name: | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase |
|---|---|
| ID: | Q8DNV6_STRR6 |
| AC: | Q8DNV6 |
| Organism: | Streptococcus pneumoniae |
| Reign: | Bacteria |
| TaxID: | 171101 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 44.698 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.068 | 2716.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.99 | 58.01 |
| According to VolSite | |
| HET Code: | 2LG |
|---|---|
| Formula: | C19H20ClN3O3S2 |
| Molecular weight: | 437.963 g/mol |
| DrugBank ID: | DB06970 |
| Buried Surface Area: | 64.53 % |
| Polar Surface area: | 126.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 17.8429 | 43.7838 | 53.6601 |
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 |
| CL19 | CD2 | PHE- 31 | 3.85 | 0 | Hydrophobic |
| C28 | CZ | PHE- 31 | 4.26 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 45 | 4.27 | 0 | Hydrophobic |
| CL19 | CB | LEU- 45 | 4.12 | 0 | Hydrophobic |
| N11 | N | ARG- 49 | 3.1 | 169.83 | H-Bond (Protein Donor) |
| C4 | CE2 | PHE- 54 | 4.19 | 0 | Hydrophobic |
| C26 | CE1 | TYR- 135 | 4.14 | 0 | Hydrophobic |
| C28 | CZ | TYR- 135 | 3.34 | 0 | Hydrophobic |
| C27 | CB | ASN- 137 | 4.2 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 139 | 4.37 | 0 | Hydrophobic |
| C26 | CG2 | ILE- 139 | 4.14 | 0 | Hydrophobic |
| S5 | CB | ASN- 328 | 3.84 | 0 | Hydrophobic |
| C4 | CG | PRO- 329 | 4.19 | 0 | Hydrophobic |
| N10 | OG1 | THR- 330 | 3.34 | 154.87 | H-Bond (Ligand Donor) |
| C15 | CB | THR- 330 | 3.73 | 0 | Hydrophobic |
| C17 | CG2 | THR- 330 | 3.69 | 0 | Hydrophobic |
| C18 | CG2 | THR- 330 | 4.02 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 360 | 4.27 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 367 | 3.49 | 0 | Hydrophobic |
