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Fluorine in PDB 8u8a: Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib

Enzymatic activity of Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib (pdb code 8u8a). 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 Ponatinib, PDB code: 8u8a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8u8a

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


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2601

b:57.0
occ:1.00
 F1 B:0LI2601 0.0 57.0 1.0
C19 B:0LI2601 1.3 53.8 1.0
F2 B:0LI2601 2.1 55.3 1.0
F3 B:0LI2601 2.2 54.8 1.0
C17 B:0LI2601 2.3 48.6 1.0
C16 B:0LI2601 3.0 46.9 1.0
CD1 B:LEU1927 3.2 79.9 1.0
C20 B:0LI2601 3.2 47.7 1.0
C18 B:0LI2601 3.4 47.8 1.0
CD1 B:LEU1932 4.3 53.6 1.0
CD2 B:LEU1985 4.3 65.3 1.0
CD2 B:LEU1932 4.3 56.7 1.0
C15 B:0LI2601 4.4 48.5 1.0
N3 B:0LI2601 4.5 53.6 1.0
CG B:LEU1927 4.7 79.7 1.0
C13 B:0LI2601 4.7 46.2 1.0
CG B:LEU1932 4.7 52.2 1.0
CD1 B:LEU1985 4.7 62.3 1.0
C21 B:0LI2601 4.8 51.3 1.0
CB B:LEU1932 4.8 48.4 1.0
CD2 B:LEU1924 4.9 65.5 1.0

Fluorine binding site 2 out of 6 in 8u8a

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


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2601

b:55.3
occ:1.00
 F2 B:0LI2601 0.0 55.3 1.0
C19 B:0LI2601 1.3 53.8 1.0
F1 B:0LI2601 2.1 57.0 1.0
F3 B:0LI2601 2.1 54.8 1.0
C17 B:0LI2601 2.4 48.6 1.0
C16 B:0LI2601 3.2 46.9 1.0
C20 B:0LI2601 3.3 47.7 1.0
C18 B:0LI2601 3.4 47.8 1.0
C21 B:0LI2601 3.8 51.3 1.0
CE1 B:TYR1992 3.8 81.0 1.0
CD1 B:TYR1992 3.9 82.1 1.0
N3 B:0LI2601 4.1 53.6 1.0
CD1 B:LEU1985 4.3 62.3 1.0
C15 B:0LI2601 4.5 48.5 1.0
CB B:ASP2017 4.5 57.7 1.0
CD2 B:LEU1932 4.6 56.7 1.0
CG2 B:ILE2015 4.6 44.2 1.0
N B:ASP2017 4.7 57.9 1.0
C13 B:0LI2601 4.7 46.2 1.0
CZ B:TYR1992 4.8 81.9 1.0
CG B:TYR1992 4.8 82.1 1.0
C B:ALA2016 5.0 53.7 1.0

Fluorine binding site 3 out of 6 in 8u8a

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


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2601

b:54.8
occ:1.00
 F3 B:0LI2601 0.0 54.8 1.0
C19 B:0LI2601 1.3 53.8 1.0
F2 B:0LI2601 2.1 55.3 1.0
F1 B:0LI2601 2.2 57.0 1.0
C17 B:0LI2601 2.3 48.6 1.0
C18 B:0LI2601 2.6 47.8 1.0
C16 B:0LI2601 3.7 46.9 1.0
O B:ILE2015 3.9 48.4 1.0
C13 B:0LI2601 4.0 46.2 1.0
CD2 B:LEU1932 4.1 56.7 1.0
C B:ILE2015 4.4 42.3 1.0
CB B:LEU1932 4.4 48.4 1.0
CA B:ALA2016 4.4 48.8 1.0
C20 B:0LI2601 4.5 47.7 1.0
O1 B:0LI2601 4.6 51.8 1.0
N B:ASP2017 4.6 57.9 1.0
N B:ILE1933 4.7 46.8 1.0
N B:ALA2016 4.7 49.7 1.0
CG B:LEU1932 4.7 52.2 1.0
C15 B:0LI2601 4.8 48.5 1.0
CD1 B:LEU1927 4.9 79.9 1.0
N2 B:0LI2601 4.9 44.5 1.0
CA B:LEU1932 4.9 48.1 1.0
C B:ALA2016 4.9 53.7 1.0
CD2 B:LEU1924 4.9 65.5 1.0
C14 B:0LI2601 4.9 47.0 1.0
CD1 B:LEU1932 5.0 53.6 1.0

Fluorine binding site 4 out of 6 in 8u8a

Go back to Fluorine Binding Sites List in 8u8a
Fluorine binding site 4 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2601

b:60.1
occ:1.00
 F1 C:0LI2601 0.0 60.1 1.0
C19 C:0LI2601 1.3 57.2 1.0
F2 C:0LI2601 2.1 58.0 1.0
F3 C:0LI2601 2.2 58.0 1.0
C17 C:0LI2601 2.3 52.5 1.0
C16 C:0LI2601 3.0 50.8 1.0
CD1 C:LEU1927 3.2 80.4 1.0
C20 C:0LI2601 3.2 52.2 1.0
C18 C:0LI2601 3.4 51.5 1.0
CD1 C:LEU1932 4.3 55.2 1.0
CD2 C:LEU1985 4.3 67.0 1.0
CD2 C:LEU1932 4.4 57.7 1.0
C15 C:0LI2601 4.4 51.6 1.0
N3 C:0LI2601 4.5 56.9 1.0
CG C:LEU1927 4.7 80.2 1.0
C13 C:0LI2601 4.7 50.1 1.0
CG C:LEU1932 4.7 53.3 1.0
CD1 C:LEU1985 4.7 64.0 1.0
C21 C:0LI2601 4.8 54.1 1.0
CB C:LEU1932 4.8 49.5 1.0
CD2 C:LEU1924 4.9 66.2 1.0

Fluorine binding site 5 out of 6 in 8u8a

Go back to Fluorine Binding Sites List in 8u8a
Fluorine binding site 5 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2601

b:58.0
occ:1.00
 F2 C:0LI2601 0.0 58.0 1.0
C19 C:0LI2601 1.3 57.2 1.0
F1 C:0LI2601 2.1 60.1 1.0
F3 C:0LI2601 2.1 58.0 1.0
C17 C:0LI2601 2.4 52.5 1.0
C16 C:0LI2601 3.1 50.8 1.0
C20 C:0LI2601 3.3 52.2 1.0
C18 C:0LI2601 3.4 51.5 1.0
C21 C:0LI2601 3.8 54.1 1.0
CE1 C:TYR1992 3.8 82.5 1.0
CD1 C:TYR1992 3.9 83.8 1.0
N3 C:0LI2601 4.1 56.9 1.0
CD1 C:LEU1985 4.3 64.0 1.0
C15 C:0LI2601 4.5 51.6 1.0
CB C:ASP2017 4.5 57.6 1.0
CD2 C:LEU1932 4.6 57.7 1.0
CG2 C:ILE2015 4.6 45.0 1.0
N C:ASP2017 4.7 57.3 1.0
C13 C:0LI2601 4.7 50.1 1.0
CZ C:TYR1992 4.8 83.0 1.0
CG C:TYR1992 4.8 83.3 1.0
C C:ALA2016 5.0 53.9 1.0
CD2 C:LEU1985 5.0 67.0 1.0

Fluorine binding site 6 out of 6 in 8u8a

Go back to Fluorine Binding Sites List in 8u8a
Fluorine binding site 6 out of 6 in the Cryo-Em Structure of LRRK2 Bound to Type II Inhibitor Ponatinib


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 Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2601

b:58.0
occ:1.00
 F3 C:0LI2601 0.0 58.0 1.0
C19 C:0LI2601 1.3 57.2 1.0
F2 C:0LI2601 2.1 58.0 1.0
F1 C:0LI2601 2.2 60.1 1.0
C17 C:0LI2601 2.3 52.5 1.0
C18 C:0LI2601 2.6 51.5 1.0
C16 C:0LI2601 3.7 50.8 1.0
O C:ILE2015 3.9 48.2 1.0
C13 C:0LI2601 4.0 50.1 1.0
CD2 C:LEU1932 4.1 57.7 1.0
C C:ILE2015 4.4 42.6 1.0
CA C:ALA2016 4.4 48.5 1.0
CB C:LEU1932 4.4 49.5 1.0
C20 C:0LI2601 4.5 52.2 1.0
O1 C:0LI2601 4.6 55.3 1.0
N C:ASP2017 4.6 57.3 1.0
N C:ILE1933 4.7 47.4 1.0
N C:ALA2016 4.7 49.1 1.0
CG C:LEU1932 4.7 53.3 1.0
C15 C:0LI2601 4.8 51.6 1.0
CD1 C:LEU1927 4.9 80.4 1.0
N2 C:0LI2601 4.9 48.5 1.0
C C:ALA2016 4.9 53.9 1.0
CA C:LEU1932 4.9 49.0 1.0
CD2 C:LEU1924 4.9 66.2 1.0
C14 C:0LI2601 4.9 50.5 1.0
CD1 C:LEU1932 5.0 55.2 1.0

Reference:

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
Page generated: Wed Jul 16 08:56:57 2025

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