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Fluorine in PDB 5i9i: Crystal Structure of LP_PLA2 in Complex with Darapladib

Enzymatic activity of Crystal Structure of LP_PLA2 in Complex with Darapladib

All present enzymatic activity of Crystal Structure of LP_PLA2 in Complex with Darapladib:
3.1.1.47;

Protein crystallography data

The structure of Crystal Structure of LP_PLA2 in Complex with Darapladib, PDB code: 5i9i was solved by Q.F.Liu, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.06 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.900, 82.410, 96.470, 90.00, 115.50, 90.00
R / Rfree (%) 19.1 / 26.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of LP_PLA2 in Complex with Darapladib (pdb code 5i9i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of LP_PLA2 in Complex with Darapladib, PDB code: 5i9i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5i9i

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Fluorine binding site 1 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:38.1
occ:1.00
 F47 A:5HV501 0.0 38.1 1.0
C46 A:5HV501 1.4 39.0 1.0
F48 A:5HV501 2.2 42.8 1.0
F49 A:5HV501 2.2 28.3 1.0
C41 A:5HV501 2.4 39.9 1.0
C39 A:5HV501 3.2 43.0 1.0
C42 A:5HV501 3.3 40.8 1.0
CD1 A:PHE357 3.3 33.9 1.0
CD1 A:LEU371 3.5 28.1 1.0
CE1 A:PHE357 3.5 30.9 1.0
CG A:PHE357 4.1 30.6 1.0
CD2 A:LEU369 4.1 40.8 1.0
CE2 A:PHE125 4.2 30.7 1.0
CZ A:PHE357 4.3 26.8 1.0
CD2 A:LEU121 4.4 32.6 1.0
CZ A:PHE125 4.4 27.4 1.0
C37 A:5HV501 4.5 46.4 1.0
C44 A:5HV501 4.5 37.9 1.0
CB A:PHE357 4.7 26.5 1.0
CG A:LEU371 4.8 30.9 1.0
CD2 A:PHE357 4.8 32.4 1.0
CD2 A:LEU371 4.9 31.4 1.0
CE2 A:PHE357 5.0 27.2 1.0
C36 A:5HV501 5.0 39.5 1.0

Fluorine binding site 2 out of 8 in 5i9i

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Fluorine binding site 2 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:42.8
occ:1.00
 F48 A:5HV501 0.0 42.8 1.0
C46 A:5HV501 1.3 39.0 1.0
F49 A:5HV501 2.2 28.3 1.0
F47 A:5HV501 2.2 38.1 1.0
C41 A:5HV501 2.4 39.9 1.0
C42 A:5HV501 2.9 40.8 1.0
CE1 A:PHE357 3.2 30.9 1.0
CD2 A:LEU121 3.2 32.6 1.0
CZ A:PHE357 3.4 26.8 1.0
C39 A:5HV501 3.6 43.0 1.0
CD1 A:PHE357 3.7 33.9 1.0
CD1 A:LEU121 3.8 34.4 1.0
CE2 A:PHE357 4.1 27.2 1.0
CG A:LEU121 4.1 39.6 1.0
CD1 A:LEU111 4.2 36.8 1.0
C44 A:5HV501 4.3 37.9 1.0
CE2 A:PHE125 4.3 30.7 1.0
CG A:PHE357 4.4 30.6 1.0
CD2 A:PHE357 4.5 32.4 1.0
CD1 A:LEU107 4.7 28.9 1.0
C37 A:5HV501 4.7 46.4 1.0
CD2 A:PHE125 4.8 25.7 1.0
CB A:LEU121 4.9 34.8 1.0

Fluorine binding site 3 out of 8 in 5i9i

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Fluorine binding site 3 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.3
occ:1.00
 F49 A:5HV501 0.0 28.3 1.0
C46 A:5HV501 1.3 39.0 1.0
F48 A:5HV501 2.2 42.8 1.0
F47 A:5HV501 2.2 38.1 1.0
C41 A:5HV501 2.3 39.9 1.0
C39 A:5HV501 2.6 43.0 1.0
CD2 A:LEU121 3.4 32.6 1.0
CD2 A:LEU369 3.5 40.8 1.0
C42 A:5HV501 3.6 40.8 1.0
C37 A:5HV501 4.0 46.4 1.0
CD1 A:LEU111 4.1 36.8 1.0
CD1 A:LEU121 4.3 34.4 1.0
CG A:LEU121 4.4 39.6 1.0
C44 A:5HV501 4.7 37.9 1.0
CD1 A:LEU371 4.8 28.1 1.0
C36 A:5HV501 4.8 39.5 1.0
CG A:LEU369 5.0 36.0 1.0

Fluorine binding site 4 out of 8 in 5i9i

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Fluorine binding site 4 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:46.6
occ:1.00
 F81 A:5HV501 0.0 46.6 1.0
C80 A:5HV501 1.3 40.0 1.0
C78 A:5HV501 2.4 36.6 1.0
C82 A:5HV501 2.4 35.6 1.0
CE2 A:PHE357 3.2 27.2 1.0
CD2 A:PHE357 3.2 32.4 1.0
CD2 A:LEU107 3.2 30.4 1.0
CD1 A:LEU159 3.3 22.6 1.0
C76 A:5HV501 3.6 28.7 1.0
C84 A:5HV501 3.7 32.2 1.0
C44 A:5HV501 3.7 37.9 1.0
C42 A:5HV501 3.9 40.8 1.0
C75 A:5HV501 4.1 35.9 1.0
CZ A:PHE357 4.4 26.8 1.0
O A:GLY154 4.4 25.6 1.0
CG A:PHE357 4.5 30.6 1.0
CG A:LEU107 4.6 32.0 1.0
CD1 A:LEU107 4.7 28.9 1.0
CG A:LEU159 4.7 23.4 1.0
C32 A:5HV501 4.9 38.8 1.0
C36 A:5HV501 5.0 39.5 1.0

Fluorine binding site 5 out of 8 in 5i9i

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Fluorine binding site 5 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:25.8
occ:1.00
 F47 B:5HV501 0.0 25.8 1.0
C46 B:5HV501 1.3 33.4 1.0
F49 B:5HV501 2.2 31.0 1.0
F48 B:5HV501 2.2 33.1 1.0
C41 B:5HV501 2.4 36.7 1.0
C39 B:5HV501 3.1 35.3 1.0
C42 B:5HV501 3.4 29.1 1.0
CD1 B:PHE357 3.6 28.3 1.0
CE1 B:PHE357 3.7 21.5 1.0
CD1 B:LEU371 3.8 18.6 1.0
CE2 B:PHE125 3.8 27.2 1.0
CZ B:PHE125 4.1 26.3 1.0
C37 B:5HV501 4.4 32.1 1.0
CG B:PHE357 4.5 31.1 1.0
CD2 B:LEU121 4.6 35.2 1.0
C44 B:5HV501 4.6 31.4 1.0
CZ B:PHE357 4.7 25.0 1.0
CG B:LEU371 4.8 25.9 1.0
CD2 B:PHE125 4.9 30.0 1.0
CD2 B:LEU371 5.0 29.4 1.0

Fluorine binding site 6 out of 8 in 5i9i

Go back to Fluorine Binding Sites List in 5i9i
Fluorine binding site 6 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:33.1
occ:1.00
 F48 B:5HV501 0.0 33.1 1.0
C46 B:5HV501 1.3 33.4 1.0
F49 B:5HV501 2.2 31.0 1.0
F47 B:5HV501 2.2 25.8 1.0
C41 B:5HV501 2.3 36.7 1.0
C42 B:5HV501 2.8 29.1 1.0
CE1 B:PHE357 3.1 21.5 1.0
CZ B:PHE357 3.4 25.0 1.0
CD2 B:LEU121 3.4 35.2 1.0
CD1 B:PHE357 3.6 28.3 1.0
C39 B:5HV501 3.6 35.3 1.0
CE2 B:PHE125 4.0 27.2 1.0
CE2 B:PHE357 4.1 22.3 1.0
C44 B:5HV501 4.2 31.4 1.0
CG B:PHE357 4.3 31.1 1.0
CD2 B:PHE125 4.5 30.0 1.0
CD2 B:PHE357 4.5 25.9 1.0
CD1 B:LEU111 4.6 25.4 1.0
CG B:LEU121 4.6 34.9 1.0
CD1 B:LEU121 4.7 31.3 1.0
C37 B:5HV501 4.8 32.1 1.0
CZ B:PHE125 4.8 26.3 1.0
C36 B:5HV501 5.0 28.7 1.0

Fluorine binding site 7 out of 8 in 5i9i

Go back to Fluorine Binding Sites List in 5i9i
Fluorine binding site 7 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:31.0
occ:1.00
 F49 B:5HV501 0.0 31.0 1.0
C46 B:5HV501 1.3 33.4 1.0
F48 B:5HV501 2.2 33.1 1.0
F47 B:5HV501 2.2 25.8 1.0
C41 B:5HV501 2.3 36.7 1.0
C39 B:5HV501 2.7 35.3 1.0
CD2 B:LEU121 3.4 35.2 1.0
C42 B:5HV501 3.5 29.1 1.0
CD1 B:LEU111 4.0 25.4 1.0
C37 B:5HV501 4.1 32.1 1.0
CG B:LEU121 4.7 34.9 1.0
C44 B:5HV501 4.7 31.4 1.0
CE2 B:PHE125 4.8 27.2 1.0
CE B:MET117 4.8 39.1 1.0
CD1 B:LEU121 4.8 31.3 1.0
C36 B:5HV501 4.9 28.7 1.0

Fluorine binding site 8 out of 8 in 5i9i

Go back to Fluorine Binding Sites List in 5i9i
Fluorine binding site 8 out of 8 in the Crystal Structure of LP_PLA2 in Complex with Darapladib


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 Darapladib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:35.7
occ:1.00
 F81 B:5HV501 0.0 35.7 1.0
C80 B:5HV501 1.3 29.6 1.0
C78 B:5HV501 2.3 25.7 1.0
C82 B:5HV501 2.4 36.3 1.0
CD2 B:PHE357 3.2 25.9 1.0
CD2 B:LEU107 3.3 28.3 1.0
CE2 B:PHE357 3.5 22.3 1.0
C44 B:5HV501 3.6 31.4 1.0
CD1 B:LEU159 3.6 20.1 1.0
C76 B:5HV501 3.6 28.7 1.0
C84 B:5HV501 3.6 27.1 1.0
C42 B:5HV501 3.9 29.1 1.0
C75 B:5HV501 4.1 27.4 1.0
CG B:PHE357 4.3 31.1 1.0
CD1 B:LEU107 4.4 34.4 1.0
CG B:LEU107 4.5 28.5 1.0
CZ B:PHE357 4.6 25.0 1.0
CB B:PHE357 4.8 22.1 1.0
C36 B:5HV501 4.8 28.7 1.0
CG B:LEU159 4.9 22.6 1.0
C32 B:5HV501 4.9 27.5 1.0
OE1 B:GLN352 4.9 34.4 1.0
O B:GLY154 5.0 22.8 1.0

Reference:

Q.F.Liu, X.D.Chen, W.Y.Chen, X.J.Yuan, H.X.Su, J.H.Shen, Y.C.Xu. Structural and Thermodynamic Characterization of Protein-Ligand Interactions Formed Between Lipoprotein-Associated Phospholipase A2 and Inhibitors J.Med.Chem. V. 59 5115 2016.
ISSN: ISSN 0022-2623
PubMed: 27078579
DOI: 10.1021/ACS.JMEDCHEM.6B00282
Page generated: Tue Jul 15 04:04:44 2025

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