sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2010-09-24
| Name: | Karilysin |
|---|---|
| ID: | KLY_TANFA |
| AC: | D0EM77 |
| Organism: | Tannerella forsythia |
| Reign: | Bacteria |
| TaxID: | 203275 |
| EC Number: | 3.4.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.293 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.750 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 51.61 | 48.39 |
| According to VolSite | |
| HET Code: | ALA_PHE_THR_SER |
|---|---|
| Formula: | C19H29N4O6 |
| Molecular weight: | 409.457 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.99 % |
| Polar Surface area: | 172.46 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 6 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -37.8273 | 18.4844 | -2.56007 |
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 |
| CB | CG2 | THR- 112 | 4.22 | 0 | Hydrophobic |
| OG | O | THR- 112 | 3.48 | 156.45 | H-Bond (Ligand Donor) |
| CB | CD1 | LEU- 115 | 4.1 | 0 | Hydrophobic |
| CD1 | CG2 | VAL- 152 | 3.96 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 155 | 3.98 | 0 | Aromatic Face/Face |
| CE1 | CB | HIS- 155 | 3.39 | 0 | Hydrophobic |
| CZ | CB | HIS- 155 | 3.43 | 0 | Hydrophobic |
| N | OE2 | GLU- 156 | 3.46 | 143.27 | H-Bond (Ligand Donor) |
| N | O | PRO- 175 | 2.95 | 136.11 | H-Bond (Ligand Donor) |
| CB | CD2 | TYR- 176 | 3.82 | 0 | Hydrophobic |
| O | N | TYR- 177 | 2.89 | 167.32 | H-Bond (Protein Donor) |
| CD2 | CB | TYR- 177 | 4.15 | 0 | Hydrophobic |
| O | ZN | ZN- 999 | 2.34 | 0 | Metal Acceptor |
