sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2010-05-19
| Name: | Beta-peptidyl aminopeptidase BapA |
|---|---|
| ID: | BAPA_SPHXN |
| AC: | Q52VH2 |
| Organism: | Sphingosinicella xenopeptidilytica |
| Reign: | Bacteria |
| TaxID: | 364098 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 4 % |
| C | 54 % |
| D | 42 % |
| B-Factor: | 15.191 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.301 | 1042.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.51 | 50.49 |
| According to VolSite | |
| HET Code: | AES |
|---|---|
| Formula: | C8H11FNO2S |
| Molecular weight: | 204.242 g/mol |
| DrugBank ID: | DB07347 |
| Buried Surface Area: | 72.23 % |
| Polar Surface area: | 70.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 3.13938 | -25.5584 | 29.2085 |
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 |
| N8 | O | THR- 76 | 2.85 | 158.88 | H-Bond (Ligand Donor) |
| C3 | CB | THR- 76 | 3.93 | 0 | Hydrophobic |
| F | CD2 | LEU- 84 | 3.8 | 0 | Hydrophobic |
| F | CD2 | LEU- 92 | 3.85 | 0 | Hydrophobic |
| C7 | CZ | PHE- 124 | 4.26 | 0 | Hydrophobic |
| C6 | CB | LEU- 127 | 4.17 | 0 | Hydrophobic |
| F | CD1 | LEU- 128 | 3.73 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 128 | 3.68 | 0 | Hydrophobic |
| N8 | OE2 | GLU- 133 | 3.24 | 0 | Ionic (Ligand Cationic) |
| N8 | OE1 | GLU- 133 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N8 | OE1 | GLU- 133 | 2.77 | 172.72 | H-Bond (Ligand Donor) |
| C7 | CB | LEU- 135 | 4.35 | 0 | Hydrophobic |
| N8 | OG | SER- 250 | 3.03 | 153.11 | H-Bond (Ligand Donor) |
| C3 | CB | LEU- 287 | 4.27 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 287 | 4.03 | 0 | Hydrophobic |
