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
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) |
|---|---|
| 0.331 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 49.68 | 50.32 |
| According to VolSite | |
| HET Code: | ON3 |
|---|---|
| Formula: | C31H33O7 |
| Molecular weight: | 517.590 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.85 % |
| Polar Surface area: | 97.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -3.79161 | -26.1611 | 49.8807 |
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 |
| C63 | CG2 | VAL- 52 | 3.88 | 0 | Hydrophobic |
| C13 | CE1 | TYR- 102 | 4.36 | 0 | Hydrophobic |
| C64 | CD2 | LEU- 105 | 4.44 | 0 | Hydrophobic |
| C63 | CE | MET- 106 | 3.82 | 0 | Hydrophobic |
| C64 | SD | MET- 106 | 3.78 | 0 | Hydrophobic |
| C64 | CB | THR- 109 | 3.99 | 0 | Hydrophobic |
| O25 | OE1 | GLN- 125 | 2.72 | 152.15 | H-Bond (Ligand Donor) |
| C13 | CG2 | ILE- 128 | 3.8 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 128 | 3.7 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 132 | 3.81 | 0 | Hydrophobic |
| C30 | SD | MET- 198 | 3.81 | 0 | Hydrophobic |
| C32 | CE | MET- 198 | 3.82 | 0 | Hydrophobic |
| C48 | CG | MET- 198 | 3.97 | 0 | Hydrophobic |
| C19 | CE2 | TYR- 202 | 4.46 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 207 | 3.83 | 0 | Hydrophobic |
| C19 | CE2 | TRP- 210 | 4.29 | 0 | Hydrophobic |
| C9 | CZ3 | TRP- 271 | 4.06 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 271 | 3.7 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 277 | 3.97 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 278 | 4.04 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 278 | 4.09 | 0 | Hydrophobic |
| C32 | CD2 | LEU- 278 | 3.83 | 0 | Hydrophobic |
| C40 | CD1 | LEU- 278 | 3.91 | 0 | Hydrophobic |
| C31 | CG | GLU- 293 | 4.44 | 0 | Hydrophobic |
| C54 | CG | GLU- 293 | 3.61 | 0 | Hydrophobic |
| C53 | CG | LYS- 294 | 4.11 | 0 | Hydrophobic |
| O70 | NZ | LYS- 294 | 2.79 | 158.72 | H-Bond (Protein Donor) |
| O70 | NZ | LYS- 294 | 2.79 | 0 | Ionic (Protein Cationic) |
| O71 | NZ | LYS- 294 | 3.27 | 0 | Ionic (Protein Cationic) |
| C43 | CB | PHE- 296 | 3.89 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 297 | 4.03 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 297 | 3.77 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 297 | 4.3 | 0 | Hydrophobic |
| C63 | CG | LEU- 297 | 4.17 | 0 | Hydrophobic |
| C54 | CD2 | LEU- 297 | 3.76 | 0 | Hydrophobic |
| C38 | CD2 | LEU- 297 | 3.85 | 0 | Hydrophobic |
| C53 | CG | LEU- 297 | 3.62 | 0 | Hydrophobic |
| C42 | CB | ALA- 300 | 4.17 | 0 | Hydrophobic |
