Fluorine in PDB 7evy: Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein

The binding sites of Fluorine atom in the Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein (pdb code 7evy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein, PDB code: 7evy:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:124.3 occ:1.00 F26 D:J8C401 0.0 124.3 1.0 C25 D:J8C401 1.4 124.3 1.0 CD2 D:LEU276 2.2 126.4 1.0 F28 D:J8C401 2.2 124.3 1.0 F27 D:J8C401 2.2 124.3 1.0 C15 D:J8C401 2.3 124.3 1.0 C14 D:J8C401 2.7 124.3 1.0 CG D:LEU276 3.5 126.4 1.0 C16 D:J8C401 3.6 124.3 1.0 CD1 D:LEU276 4.0 126.4 1.0 C13 D:J8C401 4.0 124.3 1.0 CG2 D:THR207 4.1 122.5 1.0 CB D:LEU276 4.2 126.4 1.0 C19 D:J8C401 4.3 124.3 1.0 CB D:CYS206 4.5 124.1 1.0 N D:THR207 4.7 122.5 1.0 C17 D:J8C401 4.7 124.3 1.0 O11 D:J8C401 4.8 124.3 1.0 CA D:THR207 4.8 122.5 1.0 C18 D:J8C401 4.9 124.3 1.0 C D:CYS206 4.9 124.1 1.0 CG D:LEU272 4.9 120.6 1.0 C12 D:J8C401 4.9 124.3 1.0 CD2 D:LEU272 5.0 120.6 1.0 C20 D:J8C401 5.0 124.3 1.0

Fluorine binding site 2 out of 3 in the Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:124.3 occ:1.00 F27 D:J8C401 0.0 124.3 1.0 C25 D:J8C401 1.4 124.3 1.0 F26 D:J8C401 2.2 124.3 1.0 F28 D:J8C401 2.2 124.3 1.0 C15 D:J8C401 2.4 124.3 1.0 C19 D:J8C401 2.7 124.3 1.0 C16 D:J8C401 2.8 124.3 1.0 O D:CYS206 3.2 124.1 1.0 C D:CYS206 3.3 124.1 1.0 C20 D:J8C401 3.3 124.3 1.0 C14 D:J8C401 3.6 124.3 1.0 N D:THR207 3.6 122.5 1.0 CB D:CYS206 3.6 124.1 1.0 CA D:THR207 3.8 122.5 1.0 CB D:PHE210 3.9 110.7 1.0 C24 D:J8C401 4.0 124.3 1.0 CA D:CYS206 4.0 124.1 1.0 CD2 D:LEU276 4.1 126.4 1.0 C17 D:J8C401 4.2 124.3 1.0 CG2 D:THR207 4.3 122.5 1.0 CG D:PHE210 4.5 110.7 1.0 C21 D:J8C401 4.7 124.3 1.0 CB D:THR207 4.7 122.5 1.0 C13 D:J8C401 4.7 124.3 1.0 C23 D:J8C401 4.8 124.3 1.0 C D:THR207 4.9 122.5 1.0 C22 D:J8C401 4.9 124.3 1.0 CD2 D:PHE210 5.0 110.7 1.0 C18 D:J8C401 5.0 124.3 1.0

Fluorine binding site 3 out of 3 in the Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cryo-Em Structure of Siponimod -Bound Sphingosine-1-Phosphate Receptor 1 in Complex with Gi Protein within 5.0Å range: probe atom residue distance (Å) B Occ D:F401 b:124.3 occ:1.00 F28 D:J8C401 0.0 124.3 1.0 C25 D:J8C401 1.4 124.3 1.0 F26 D:J8C401 2.2 124.3 1.0 F27 D:J8C401 2.2 124.3 1.0 C15 D:J8C401 2.3 124.3 1.0 C14 D:J8C401 3.1 124.3 1.0 C16 D:J8C401 3.3 124.3 1.0 C19 D:J8C401 3.6 124.3 1.0 CD2 D:LEU276 4.1 126.4 1.0 CG D:PHE210 4.2 110.7 1.0 CD2 D:PHE210 4.3 110.7 1.0 C13 D:J8C401 4.3 124.3 1.0 CB D:PHE210 4.3 110.7 1.0 CD2 D:LEU272 4.4 120.6 1.0 C24 D:J8C401 4.4 124.3 1.0 C17 D:J8C401 4.4 124.3 1.0 CZ3 D:TRP269 4.5 107.7 1.0 CG D:LEU272 4.6 120.6 1.0 CE3 D:TRP269 4.6 107.7 1.0 CD1 D:PHE210 4.6 110.7 1.0 CA D:PHE273 4.8 120.3 1.0 CE2 D:PHE210 4.8 110.7 1.0 C20 D:J8C401 4.9 124.3 1.0 CD1 D:PHE273 4.9 120.3 1.0 C18 D:J8C401 4.9 124.3 1.0 CG2 D:THR207 4.9 122.5 1.0 N D:PHE273 4.9 120.3 1.0 CB D:PHE273 5.0 120.3 1.0 CA D:THR207 5.0 122.5 1.0

Y.Yuan, G.Jia, C.Wu, W.Wang, L.Cheng, Q.Li, Z.Li, K.Luo, S.Yang, W.Yan, Z.Su, Z.Shao. Structures of Signaling Complexes of Lipid Receptors S1PR1 and S1PR5 Reveal Mechanisms of Activation and Drug Recognition. Cell Res. 2021.
ISSN: ISSN 1001-0602
PubMed: 34526663
DOI: 10.1038/S41422-021-00566-X