Fluorine in PDB 6m07: Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor

Enzymatic activity of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor

All present enzymatic activity of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor:
3.1.1.47;

Protein crystallography data

The structure of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor, PDB code: 6m07 was solved by H.C.Hu, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 2.64
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.687, 77.857, 94.698, 90, 115.32, 90
R / Rfree (%) 20 / 24.9

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor (pdb code 6m07). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor, PDB code: 6m07:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6m07

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Fluorine binding site 1 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:70.4
occ:1.00
 F37 A:BWO501 0.0 70.4 1.0
C36 A:BWO501 1.3 76.3 1.0
F38 A:BWO501 2.1 85.8 1.0
F39 A:BWO501 2.2 76.1 1.0
C33 A:BWO501 2.3 70.0 1.0
C32 A:BWO501 2.6 66.8 1.0
CE1 A:PHE357 2.9 56.8 1.0
CD1 A:PHE357 3.3 51.7 1.0
CZ A:PHE357 3.3 56.1 1.0
C34 A:BWO501 3.6 67.9 1.0
CD2 A:LEU121 3.8 68.9 1.0
CE2 A:PHE357 4.0 53.3 1.0
CG A:PHE357 4.0 45.7 1.0
C31 A:BWO501 4.0 68.6 1.0
CE2 A:PHE125 4.2 41.5 1.0
CD2 A:PHE357 4.3 49.8 1.0
CZ A:PHE125 4.5 38.4 1.0
CD1 A:LEU371 4.6 53.0 1.0
C35 A:BWO501 4.7 65.1 1.0
C41 A:BWO501 4.8 70.6 1.0
O40 A:BWO501 4.9 68.4 1.0
C30 A:BWO501 4.9 67.0 1.0
CD2 A:PHE125 5.0 43.0 1.0
CB A:PHE357 5.0 41.5 1.0

Fluorine binding site 2 out of 12 in 6m07

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Fluorine binding site 2 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:85.8
occ:1.00
 F38 A:BWO501 0.0 85.8 1.0
C36 A:BWO501 1.3 76.3 1.0
F37 A:BWO501 2.1 70.4 1.0
F39 A:BWO501 2.2 76.1 1.0
C33 A:BWO501 2.3 70.0 1.0
C34 A:BWO501 3.0 67.9 1.0
CD2 A:LEU121 3.1 68.9 1.0
C32 A:BWO501 3.3 66.8 1.0
CD1 A:LEU121 4.2 66.4 1.0
C35 A:BWO501 4.2 65.1 1.0
CG A:LEU121 4.3 65.7 1.0
CG A:LEU111 4.3 57.1 1.0
C31 A:BWO501 4.5 68.6 1.0
CE A:MET117 4.5 91.5 1.0
C30 A:BWO501 4.8 67.0 1.0
CE1 A:PHE357 5.0 56.8 1.0

Fluorine binding site 3 out of 12 in 6m07

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Fluorine binding site 3 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:76.1
occ:1.00
 F39 A:BWO501 0.0 76.1 1.0
C36 A:BWO501 1.3 76.3 1.0
F37 A:BWO501 2.2 70.4 1.0
F38 A:BWO501 2.2 85.8 1.0
C33 A:BWO501 2.3 70.0 1.0
C34 A:BWO501 2.8 67.9 1.0
C32 A:BWO501 3.4 66.8 1.0
CD1 A:LEU371 3.7 53.0 1.0
C35 A:BWO501 4.1 65.1 1.0
CD2 A:LEU121 4.3 68.9 1.0
C31 A:BWO501 4.5 68.6 1.0
CD1 A:PHE357 4.6 51.7 1.0
CE1 A:PHE357 4.6 56.8 1.0
CE2 A:PHE125 4.6 41.5 1.0
CZ A:PHE125 4.6 38.4 1.0
CG A:LEU369 4.7 57.5 1.0
CG A:LEU371 4.7 51.1 1.0
C30 A:BWO501 4.8 67.0 1.0
CB A:LEU369 4.9 56.5 1.0
CD2 A:LEU371 5.0 51.2 1.0

Fluorine binding site 4 out of 12 in 6m07

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Fluorine binding site 4 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:74.9
occ:1.00
 F43 A:BWO501 0.0 74.9 1.0
C42 A:BWO501 1.3 76.4 1.0
F46 A:BWO501 2.2 84.3 1.0
F44 A:BWO501 2.2 71.8 1.0
C41 A:BWO501 2.3 70.6 1.0
CD1 A:LEU159 3.2 30.6 1.0
O40 A:BWO501 3.5 68.4 1.0
NE2 A:GLN352 3.8 38.0 1.0
CD2 A:PHE357 3.9 49.8 1.0
CE2 A:PHE357 4.2 53.3 1.0
O A:GLY154 4.3 28.0 1.0
CA A:ALA155 4.4 31.6 1.0
CD2 A:LEU107 4.5 39.9 1.0
CB A:ALA155 4.6 31.4 1.0
C A:GLY154 4.6 30.7 1.0
CG A:LEU159 4.6 31.7 1.0
N A:ALA155 4.6 31.5 1.0
CD A:GLN352 4.7 39.2 1.0
C31 A:BWO501 4.8 68.6 1.0
CB A:LEU159 4.9 31.6 1.0

Fluorine binding site 5 out of 12 in 6m07

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Fluorine binding site 5 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:71.8
occ:1.00
 F44 A:BWO501 0.0 71.8 1.0
C42 A:BWO501 1.3 76.4 1.0
F46 A:BWO501 2.1 84.3 1.0
F43 A:BWO501 2.2 74.9 1.0
C41 A:BWO501 2.3 70.6 1.0
O40 A:BWO501 2.5 68.4 1.0
NE2 A:GLN352 2.9 38.0 1.0
CD A:GLN352 3.3 39.2 1.0
OE1 A:GLN352 3.4 36.0 1.0
C26 A:BWO501 3.6 68.0 1.0
C31 A:BWO501 3.9 68.6 1.0
C25 A:BWO501 4.0 68.2 1.0
CE2 A:PHE110 4.1 34.9 1.0
C27 A:BWO501 4.3 66.3 1.0
CG A:GLN352 4.3 39.5 1.0
C30 A:BWO501 4.6 67.0 1.0
CZ A:PHE110 4.8 34.2 1.0
C32 A:BWO501 4.8 66.8 1.0
O A:LEU153 4.9 30.5 1.0

Fluorine binding site 6 out of 12 in 6m07

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Fluorine binding site 6 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:84.3
occ:1.00
 F46 A:BWO501 0.0 84.3 1.0
C42 A:BWO501 1.3 76.4 1.0
F44 A:BWO501 2.1 71.8 1.0
F43 A:BWO501 2.2 74.9 1.0
C41 A:BWO501 2.4 70.6 1.0
CE2 A:PHE110 2.9 34.9 1.0
O40 A:BWO501 3.0 68.4 1.0
CD2 A:PHE110 3.4 35.3 1.0
O A:GLY154 3.5 28.0 1.0
CD2 A:LEU107 3.7 39.9 1.0
C A:GLY154 3.8 30.7 1.0
CZ A:PHE110 3.9 34.2 1.0
C31 A:BWO501 4.2 68.6 1.0
C26 A:BWO501 4.3 68.0 1.0
CA A:GLY154 4.3 31.6 1.0
N A:ALA155 4.4 31.5 1.0
O A:LEU153 4.5 30.5 1.0
CG A:PHE110 4.7 38.3 1.0
C32 A:BWO501 4.8 66.8 1.0
CA A:ALA155 4.8 31.6 1.0
NE2 A:GLN352 4.8 38.0 1.0
CD1 A:LEU159 4.9 30.6 1.0
C25 A:BWO501 5.0 68.2 1.0

Fluorine binding site 7 out of 12 in 6m07

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Fluorine binding site 7 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:68.0
occ:1.00
 F37 B:BWO501 0.0 68.0 1.0
C36 B:BWO501 1.3 68.4 1.0
F39 B:BWO501 2.1 64.7 1.0
F38 B:BWO501 2.2 66.5 1.0
C33 B:BWO501 2.4 76.6 1.0
C32 B:BWO501 2.8 77.7 1.0
CD2 B:LEU121 3.2 50.4 1.0
CE1 B:PHE357 3.5 35.9 1.0
C34 B:BWO501 3.6 82.0 1.0
CZ B:PHE357 3.9 37.6 1.0
CD1 B:PHE357 4.0 35.1 1.0
C31 B:BWO501 4.2 81.8 1.0
CD1 B:LEU121 4.2 56.4 1.0
CG B:LEU121 4.3 55.8 1.0
CE2 B:PHE357 4.5 37.2 1.0
CG B:PHE357 4.6 37.1 1.0
C35 B:BWO501 4.8 83.5 1.0
CD2 B:PHE357 4.9 39.0 1.0
CE2 B:PHE125 4.9 61.5 1.0
O40 B:BWO501 5.0 79.4 1.0

Fluorine binding site 8 out of 12 in 6m07

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Fluorine binding site 8 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:66.5
occ:1.00
 F38 B:BWO501 0.0 66.5 1.0
C36 B:BWO501 1.3 68.4 1.0
F39 B:BWO501 2.0 64.7 1.0
F37 B:BWO501 2.2 68.0 1.0
C33 B:BWO501 2.3 76.6 1.0
C34 B:BWO501 2.8 82.0 1.0
C32 B:BWO501 3.6 77.7 1.0
CD2 B:LEU121 3.9 50.4 1.0
CD1 B:LEU369 4.0 50.1 1.0
C35 B:BWO501 4.1 83.5 1.0
C31 B:BWO501 4.7 81.8 1.0
CG B:LEU121 4.9 55.8 1.0
CD1 B:LEU121 4.9 56.4 1.0
C30 B:BWO501 5.0 86.0 1.0

Fluorine binding site 9 out of 12 in 6m07

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Fluorine binding site 9 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:64.7
occ:1.00
 F39 B:BWO501 0.0 64.7 1.0
C36 B:BWO501 1.3 68.4 1.0
F38 B:BWO501 2.0 66.5 1.0
F37 B:BWO501 2.1 68.0 1.0
C33 B:BWO501 2.3 76.6 1.0
C34 B:BWO501 3.1 82.0 1.0
C32 B:BWO501 3.2 77.7 1.0
CD1 B:LEU371 3.4 47.0 1.0
CD1 B:LEU369 3.8 50.1 1.0
CD1 B:PHE357 4.1 35.1 1.0
CE1 B:PHE357 4.2 35.9 1.0
C35 B:BWO501 4.4 83.5 1.0
CD2 B:LEU121 4.4 50.4 1.0
C31 B:BWO501 4.5 81.8 1.0
CG B:LEU371 4.5 45.9 1.0
CD2 B:LEU371 4.7 43.7 1.0
CG B:PHE357 4.8 37.1 1.0
CG2 B:THR361 4.9 52.8 1.0
C30 B:BWO501 5.0 86.0 1.0
CG B:LEU369 5.0 49.5 1.0
CE2 B:PHE125 5.0 61.5 1.0

Fluorine binding site 10 out of 12 in 6m07

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Fluorine binding site 10 out of 12 in the Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Lp-PLA2 in Complex with A Novel Covalent Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:84.3
occ:1.00
 F43 B:BWO501 0.0 84.3 1.0
C42 B:BWO501 1.3 88.0 1.0
F46 B:BWO501 2.2 97.3 1.0
F44 B:BWO501 2.2 81.4 1.0
C41 B:BWO501 2.4 86.8 1.0
O40 B:BWO501 2.7 79.4 1.0
CD2 B:PHE357 3.3 39.0 1.0
OE1 B:GLN352 3.3 55.4 1.0
CD B:GLN352 3.9 48.8 1.0
C31 B:BWO501 4.0 81.8 1.0
CB B:PHE357 4.0 36.3 1.0
CG B:PHE357 4.0 37.1 1.0
CE2 B:PHE357 4.1 37.2 1.0
NE2 B:GLN352 4.1 46.1 1.0
CD1 B:LEU159 4.5 33.8 1.0
C32 B:BWO501 4.5 77.7 1.0
CB B:ALA355 4.7 34.0 1.0

Reference:

F.Huang, H.Hu, K.Wang, C.Peng, W.Xu, Y.Zhang, J.Gao, Y.Liu, H.Zhou, R.Huang, M.Li, J.Shen, Y.Xu. Identification of Highly Selective Lipoprotein-Associated Phospholipase A2 (Lp-PLA2) Inhibitors By A Covalent Fragment-Based Approach. J.Med.Chem. V. 63 7052 2020.
ISSN: ISSN 0022-2623
PubMed: 32459096
DOI: 10.1021/ACS.JMEDCHEM.0C00372
Page generated: Sun Jan 24 15:48:48 2021

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