Fluorine in PDB 8u7l: Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824

All present enzymatic activity of Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824:
2.7.11.1;

The binding sites of Fluorine atom in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824 (pdb code 8u7l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824, PDB code: 8u7l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


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 LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2602 b:72.4 occ:1.00 F26 B:T3X2602 0.0 72.4 1.0 C25 B:T3X2602 1.4 72.4 1.0 F27 B:T3X2602 2.2 72.4 1.0 F28 B:T3X2602 2.2 72.4 1.0 C13 B:T3X2602 2.4 72.4 1.0 C14 B:T3X2602 3.0 72.4 1.0 C17 B:T3X2602 3.1 72.4 1.0 C12 B:T3X2602 3.4 72.4 1.0 CG2 B:ILE2015 3.8 62.4 1.0 CE1 B:TYR1992 4.0 84.8 1.0 CD1 B:TYR1992 4.0 84.8 1.0 CD1 B:LEU1985 4.2 76.8 1.0 N18 B:T3X2602 4.2 72.4 1.0 C15 B:T3X2602 4.3 72.4 1.0 C23 B:T3X2602 4.4 72.4 1.0 O B:ILE2015 4.4 62.4 1.0 CB B:ASP2017 4.5 71.5 1.0 N B:ASP2017 4.6 71.5 1.0 C11 B:T3X2602 4.6 72.4 1.0 CD2 B:LEU1932 4.6 69.7 1.0 CZ B:TYR1992 4.6 84.8 1.0 C B:ILE2015 4.7 62.4 1.0 CG B:TYR1992 4.8 84.8 1.0 CA B:ALA2016 4.8 68.7 1.0 C B:ALA2016 4.8 68.7 1.0 CB B:ILE2015 4.9 62.4 1.0 N B:ALA2016 4.9 68.7 1.0 C16 B:T3X2602 5.0 72.4 1.0 CD2 B:LEU1985 5.0 76.8 1.0

Fluorine binding site 2 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


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 LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2602 b:72.4 occ:1.00 F27 B:T3X2602 0.0 72.4 1.0 C25 B:T3X2602 1.4 72.4 1.0 F28 B:T3X2602 2.2 72.4 1.0 F26 B:T3X2602 2.2 72.4 1.0 C13 B:T3X2602 2.3 72.4 1.0 C12 B:T3X2602 2.6 72.4 1.0 O B:ILE2015 3.4 62.4 1.0 C14 B:T3X2602 3.7 72.4 1.0 C11 B:T3X2602 4.0 72.4 1.0 C B:ILE2015 4.2 62.4 1.0 CA B:ALA2016 4.3 68.7 1.0 CD2 B:LEU1932 4.3 69.7 1.0 CB B:LEU1932 4.4 69.7 1.0 C17 B:T3X2602 4.4 72.4 1.0 N B:ILE1933 4.5 62.5 1.0 O09 B:T3X2602 4.6 72.4 1.0 N B:ALA2016 4.7 68.7 1.0 N B:ASP2017 4.7 71.5 1.0 CG2 B:ILE2015 4.7 62.4 1.0 C15 B:T3X2602 4.8 72.4 1.0 CD1 B:LEU1927 4.8 90.3 1.0 CA B:LEU1932 4.8 69.7 1.0 N10 B:T3X2602 4.8 72.4 1.0 CG B:LEU1932 4.9 69.7 1.0 C16 B:T3X2602 4.9 72.4 1.0 C B:ALA2016 4.9 68.7 1.0

Fluorine binding site 3 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


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 LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2602 b:72.4 occ:1.00 F28 B:T3X2602 0.0 72.4 1.0 C25 B:T3X2602 1.4 72.4 1.0 F27 B:T3X2602 2.2 72.4 1.0 F26 B:T3X2602 2.2 72.4 1.0 C13 B:T3X2602 2.4 72.4 1.0 C14 B:T3X2602 3.0 72.4 1.0 C17 B:T3X2602 3.1 72.4 1.0 CD1 B:LEU1927 3.2 90.3 1.0 C12 B:T3X2602 3.4 72.4 1.0 CD2 B:LEU1985 4.2 76.8 1.0 C15 B:T3X2602 4.3 72.4 1.0 N18 B:T3X2602 4.4 72.4 1.0 CD2 B:LEU1932 4.5 69.7 1.0 CD1 B:LEU1932 4.6 69.7 1.0 C11 B:T3X2602 4.6 72.4 1.0 CD1 B:LEU1985 4.6 76.8 1.0 CG B:LEU1927 4.7 90.3 1.0 C19 B:T3X2602 4.9 72.4 1.0 CG B:LEU1985 4.9 76.8 1.0 CG B:LEU1932 4.9 69.7 1.0 CB B:LEU1932 5.0 69.7 1.0 C16 B:T3X2602 5.0 72.4 1.0

Fluorine binding site 4 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2602 b:89.5 occ:1.00 F26 A:T3X2602 0.0 89.5 1.0 C25 A:T3X2602 1.4 89.5 1.0 F27 A:T3X2602 2.2 89.5 1.0 F28 A:T3X2602 2.2 89.5 1.0 C13 A:T3X2602 2.4 89.5 1.0 C14 A:T3X2602 3.0 89.5 1.0 C17 A:T3X2602 3.1 89.5 1.0 C12 A:T3X2602 3.4 89.5 1.0 CG2 A:ILE2015 3.9 86.4 1.0 CE1 A:TYR1992 4.1 108.2 1.0 CD1 A:TYR1992 4.1 108.2 1.0 CD1 A:LEU1985 4.2 100.9 1.0 N18 A:T3X2602 4.2 89.5 1.0 C23 A:T3X2602 4.3 89.5 1.0 C15 A:T3X2602 4.3 89.5 1.0 O A:ILE2015 4.4 86.4 1.0 CB A:ASP2017 4.5 94.4 1.0 N A:ASP2017 4.6 94.4 1.0 C11 A:T3X2602 4.6 89.5 1.0 CD2 A:LEU1932 4.6 92.2 1.0 C A:ILE2015 4.8 86.4 1.0 CZ A:TYR1992 4.8 108.2 1.0 CA A:ALA2016 4.8 91.3 1.0 C A:ALA2016 4.9 91.3 1.0 CG A:TYR1992 4.9 108.2 1.0 CB A:ILE2015 4.9 86.4 1.0 N A:ALA2016 5.0 91.3 1.0 CD2 A:LEU1985 5.0 100.9 1.0 C16 A:T3X2602 5.0 89.5 1.0

Fluorine binding site 5 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2602 b:89.5 occ:1.00 F27 A:T3X2602 0.0 89.5 1.0 C25 A:T3X2602 1.4 89.5 1.0 F28 A:T3X2602 2.2 89.5 1.0 F26 A:T3X2602 2.2 89.5 1.0 C13 A:T3X2602 2.3 89.5 1.0 C12 A:T3X2602 2.6 89.5 1.0 O A:ILE2015 3.5 86.4 1.0 C14 A:T3X2602 3.7 89.5 1.0 C11 A:T3X2602 4.0 89.5 1.0 C A:ILE2015 4.4 86.4 1.0 CB A:LEU1932 4.4 92.2 1.0 CA A:ALA2016 4.4 91.3 1.0 C17 A:T3X2602 4.4 89.5 1.0 CD2 A:LEU1932 4.4 92.2 1.0 N A:ILE1933 4.5 85.1 1.0 O09 A:T3X2602 4.6 89.5 1.0 N A:ASP2017 4.7 94.4 1.0 CD1 A:LEU1927 4.7 107.8 1.0 C15 A:T3X2602 4.8 89.5 1.0 N A:ALA2016 4.8 91.3 1.0 CG2 A:ILE2015 4.8 86.4 1.0 N10 A:T3X2602 4.8 89.5 1.0 CA A:LEU1932 4.8 92.2 1.0 C16 A:T3X2602 4.9 89.5 1.0 CG A:LEU1932 4.9 92.2 1.0 O A:ILE1933 5.0 85.1 1.0 C A:ALA2016 5.0 91.3 1.0

Fluorine binding site 6 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor GZD824 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2602 b:89.5 occ:1.00 F28 A:T3X2602 0.0 89.5 1.0 C25 A:T3X2602 1.4 89.5 1.0 F27 A:T3X2602 2.2 89.5 1.0 F26 A:T3X2602 2.2 89.5 1.0 C13 A:T3X2602 2.4 89.5 1.0 C14 A:T3X2602 3.0 89.5 1.0 C17 A:T3X2602 3.1 89.5 1.0 CD1 A:LEU1927 3.2 107.8 1.0 C12 A:T3X2602 3.4 89.5 1.0 CD2 A:LEU1985 4.3 100.9 1.0 C15 A:T3X2602 4.3 89.5 1.0 N18 A:T3X2602 4.4 89.5 1.0 CD2 A:LEU1932 4.6 92.2 1.0 CD1 A:LEU1932 4.6 92.2 1.0 C11 A:T3X2602 4.6 89.5 1.0 CG A:LEU1927 4.7 107.8 1.0 CD1 A:LEU1985 4.7 100.9 1.0 C19 A:T3X2602 4.9 89.5 1.0 CG A:LEU1932 5.0 92.2 1.0 CG A:LEU1985 5.0 100.9 1.0 CB A:LEU1932 5.0 92.2 1.0 C16 A:T3X2602 5.0 89.5 1.0

H.Zhu, P.Hixson, W.Ma, J.Sun. Pharmacology of LRRK2 with Type I and II Kinase Inhibitors Revealed By Cryo-Em. Cell Discov V. 10 10 2024.
ISSN: ESSN 2056-5968
PubMed: 38263358
DOI: 10.1038/S41421-023-00639-8