sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2015-03-30
| Name: | Lysophosphatidic acid receptor 1 |
|---|---|
| ID: | LPAR1_HUMAN |
| AC: | Q92633 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 793.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.87 | 42.13 |
| According to VolSite | |
| HET Code: | ON7 |
|---|---|
| Formula: | C30H34NO7 |
| Molecular weight: | 520.593 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.12 % |
| Polar Surface area: | 110.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -3.41234 | -26.2543 | 50.8203 |
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 |
| O6 | NZ | LYS- 39 | 2.8 | 0 | Ionic (Protein Cationic) |
| DuAr | NZ | LYS- 39 | 3.68 | 22.74 | Pi/Cation |
| O6 | NE2 | HIS- 40 | 3.39 | 139.53 | H-Bond (Protein Donor) |
| C29 | CG1 | VAL- 52 | 3.65 | 0 | Hydrophobic |
| C4 | CE1 | TYR- 102 | 4.27 | 0 | Hydrophobic |
| C30 | CD1 | LEU- 105 | 4.04 | 0 | Hydrophobic |
| C29 | SD | MET- 106 | 4.27 | 0 | Hydrophobic |
| C29 | CG2 | THR- 109 | 3.73 | 0 | Hydrophobic |
| C30 | CG2 | THR- 109 | 4.33 | 0 | Hydrophobic |
| O7 | OG1 | THR- 113 | 3.39 | 149.54 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 125 | 2.95 | 127.13 | H-Bond (Protein Donor) |
| C4 | CG2 | ILE- 128 | 4.09 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 128 | 3.55 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 132 | 3.36 | 0 | Hydrophobic |
| C14 | SD | MET- 198 | 3.69 | 0 | Hydrophobic |
| C16 | CE | MET- 198 | 3.7 | 0 | Hydrophobic |
| C13 | CG | MET- 198 | 3.55 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 207 | 3.84 | 0 | Hydrophobic |
| C10 | CZ3 | TRP- 271 | 4.07 | 0 | Hydrophobic |
| C4 | CZ3 | TRP- 271 | 3.49 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 277 | 3.85 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 278 | 3.83 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 278 | 4.4 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 278 | 3.6 | 0 | Hydrophobic |
| C22 | CB | PHE- 296 | 4.17 | 0 | Hydrophobic |
| C15 | CB | PHE- 296 | 4.28 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 297 | 3.87 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 297 | 4.12 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 297 | 3.38 | 0 | Hydrophobic |
| C21 | CB | ALA- 300 | 4.32 | 0 | Hydrophobic |
