sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.900 Å
X-ray
2010-03-24
| Name: | Putative sphingosine-1-phosphate lyase |
|---|---|
| ID: | Q67PY4_SYMTH |
| AC: | Q67PY4 |
| Organism: | Symbiobacterium thermophilum |
| Reign: | Bacteria |
| TaxID: | 292459 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 78 % |
| B | 22 % |
| B-Factor: | 60.455 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.257 | 1194.750 |
| % Hydrophobic | % Polar |
|---|---|
| 51.98 | 48.02 |
| According to VolSite | |
| HET Code: | PLR |
|---|---|
| Formula: | C8H10NO5P |
| Molecular weight: | 231.142 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 73.79 % |
| Polar Surface area: | 115.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -4.99233 | -39.6943 | 23.5016 |
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 |
| O2P | N | GLY- 168 | 3.43 | 146.66 | H-Bond (Protein Donor) |
| O3P | OG1 | THR- 169 | 3.04 | 146.05 | H-Bond (Protein Donor) |
| O3P | N | THR- 169 | 2.73 | 167.14 | H-Bond (Protein Donor) |
| DuAr | DuAr | HIS- 201 | 3.98 | 0 | Aromatic Face/Face |
| C2A | CB | TYR- 249 | 3.59 | 0 | Hydrophobic |
| C3 | CB | TYR- 249 | 4.2 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 274 | 3.02 | 159.99 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 274 | 3.2 | 131.43 | H-Bond (Ligand Donor) |
| C5 | CB | CYS- 276 | 4.11 | 0 | Hydrophobic |
| C2A | CB | LEU- 277 | 3.76 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 277 | 4.29 | 0 | Hydrophobic |
| O2P | NE2 | HIS- 310 | 2.96 | 126.85 | H-Bond (Protein Donor) |
| O1P | N | SER- 353 | 3.32 | 151.97 | H-Bond (Protein Donor) |
| O1P | OG | SER- 353 | 3.3 | 156.01 | H-Bond (Protein Donor) |
| O3P | O | HOH- 522 | 2.63 | 136.41 | H-Bond (Protein Donor) |
