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Fluorine in PDB 6g5j: Secreted Phospholipase A2 Type X in Complex with Ligand

Enzymatic activity of Secreted Phospholipase A2 Type X in Complex with Ligand

All present enzymatic activity of Secreted Phospholipase A2 Type X in Complex with Ligand:
3.1.1.4;

Protein crystallography data

The structure of Secreted Phospholipase A2 Type X in Complex with Ligand, PDB code: 6g5j was solved by J.Sandmark, L.Oster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.76 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.962, 85.501, 103.079, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.8

Other elements in 6g5j:

The structure of Secreted Phospholipase A2 Type X in Complex with Ligand also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Secreted Phospholipase A2 Type X in Complex with Ligand (pdb code 6g5j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Secreted Phospholipase A2 Type X in Complex with Ligand, PDB code: 6g5j:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 6g5j

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Fluorine binding site 1 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.5
occ:0.50
 F27 A:EM8202 0.0 21.5 0.5
F27 A:EM8202 1.2 20.7 0.5
C26 A:EM8202 1.4 20.8 0.5
C26 A:EM8202 1.9 20.2 0.5
O25 A:EM8202 2.0 18.9 0.5
F29 A:EM8202 2.3 21.7 0.5
O25 A:EM8202 2.3 20.7 0.5
F28 A:EM8202 2.3 21.5 0.5
F29 A:EM8202 2.8 21.5 0.5
F28 A:EM8202 3.0 21.3 0.5
C16 A:EM8202 3.4 17.5 0.5
C16 A:EM8202 3.5 18.9 0.5
O A:PRO17 3.6 21.3 1.0
CB A:PRO17 3.6 20.5 1.0
C A:PRO17 3.6 20.2 1.0
N A:ILE18 3.9 21.7 1.0
CG A:MET21 3.9 25.2 0.5
CG A:MET21 4.1 26.8 0.5
SD A:MET21 4.1 26.9 0.5
CG A:PRO17 4.2 21.0 1.0
C15 A:EM8202 4.2 18.5 0.5
CB A:ALA6 4.2 17.2 1.0
C17 A:EM8202 4.2 16.8 0.5
C15 A:EM8202 4.2 17.1 0.5
CA A:PRO17 4.3 20.6 1.0
SD A:MET21 4.3 29.5 0.5
CA A:ILE18 4.4 22.8 1.0
C17 A:EM8202 4.6 18.3 0.5
CA A:ALA6 4.7 17.1 1.0

Fluorine binding site 2 out of 12 in 6g5j

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Fluorine binding site 2 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:20.7
occ:0.50
 F27 A:EM8202 0.0 20.7 0.5
F27 A:EM8202 1.2 21.5 0.5
C26 A:EM8202 1.4 20.2 0.5
C26 A:EM8202 1.7 20.8 0.5
F28 A:EM8202 1.9 21.5 0.5
F29 A:EM8202 2.3 21.5 0.5
F28 A:EM8202 2.3 21.3 0.5
O25 A:EM8202 2.3 18.9 0.5
O25 A:EM8202 2.4 20.7 0.5
F29 A:EM8202 3.0 21.7 0.5
CB A:ALA6 3.4 17.2 1.0
C16 A:EM8202 3.6 17.5 0.5
C16 A:EM8202 3.7 18.9 0.5
CA A:ALA6 4.0 17.1 1.0
CB A:PRO17 4.1 20.5 1.0
C15 A:EM8202 4.2 18.5 0.5
C15 A:EM8202 4.3 17.1 0.5
C17 A:EM8202 4.5 16.8 0.5
N A:ALA6 4.5 16.5 1.0
CG A:PRO17 4.5 21.0 1.0
CG2 A:ILE2 4.6 19.6 0.5
O A:PRO17 4.6 21.3 1.0
O A:ILE2 4.7 19.0 1.0
C A:PRO17 4.7 20.2 1.0
C17 A:EM8202 4.8 18.3 0.5
SD A:MET21 4.8 29.5 0.5
CG A:MET21 4.8 25.2 0.5
SD A:MET21 4.9 26.9 0.5
CG A:MET21 4.9 26.8 0.5

Fluorine binding site 3 out of 12 in 6g5j

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Fluorine binding site 3 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.5
occ:0.50
 F28 A:EM8202 0.0 21.5 0.5
F29 A:EM8202 0.5 21.5 0.5
C26 A:EM8202 1.0 20.2 0.5
C26 A:EM8202 1.4 20.8 0.5
F27 A:EM8202 1.9 20.7 0.5
O25 A:EM8202 1.9 18.9 0.5
F28 A:EM8202 2.1 21.3 0.5
F27 A:EM8202 2.3 21.5 0.5
F29 A:EM8202 2.3 21.7 0.5
O25 A:EM8202 2.3 20.7 0.5
C16 A:EM8202 2.7 17.5 0.5
C15 A:EM8202 2.9 17.1 0.5
C15 A:EM8202 2.9 18.5 0.5
C16 A:EM8202 2.9 18.9 0.5
SD A:MET21 3.9 29.5 0.5
C17 A:EM8202 3.9 16.8 0.5
CG2 A:ILE2 4.1 19.6 0.5
C14 A:EM8202 4.2 16.8 0.5
C14 A:EM8202 4.2 18.0 0.5
C17 A:EM8202 4.3 18.3 0.5
CG A:MET21 4.4 26.8 0.5
CG A:MET21 4.4 25.2 0.5
C10 A:EM8202 4.7 19.7 0.5
CB A:ALA6 4.8 17.2 1.0
SD A:MET21 4.8 26.9 0.5
CD2 A:LEU5 4.8 16.4 1.0
C10 A:EM8202 4.9 18.8 0.5
O A:ILE2 4.9 19.0 1.0
O A:PRO17 4.9 21.3 1.0
C18 A:EM8202 5.0 16.5 0.5

Fluorine binding site 4 out of 12 in 6g5j

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Fluorine binding site 4 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.3
occ:0.50
 F28 A:EM8202 0.0 21.3 0.5
C26 A:EM8202 1.4 20.2 0.5
O25 A:EM8202 2.0 20.7 0.5
F28 A:EM8202 2.1 21.5 0.5
F27 A:EM8202 2.3 20.7 0.5
F29 A:EM8202 2.3 21.5 0.5
O25 A:EM8202 2.3 18.9 0.5
C26 A:EM8202 2.4 20.8 0.5
C16 A:EM8202 2.6 18.9 0.5
C16 A:EM8202 2.7 17.5 0.5
F27 A:EM8202 3.0 21.5 0.5
C15 A:EM8202 3.1 18.5 0.5
N A:ALA6 3.1 16.5 1.0
CA A:ALA6 3.3 17.1 1.0
C17 A:EM8202 3.3 16.8 0.5
C15 A:EM8202 3.3 17.1 0.5
C17 A:EM8202 3.4 18.3 0.5
CB A:ALA6 3.5 17.2 1.0
CG A:LEU5 3.5 15.8 1.0
C A:LEU5 3.7 15.9 1.0
F29 A:EM8202 3.7 21.7 0.5
O A:ILE2 3.8 19.0 1.0
CB A:LEU5 3.8 16.0 1.0
CD2 A:LEU5 3.8 16.4 1.0
O A:LEU5 4.2 14.8 1.0
C14 A:EM8202 4.2 18.0 0.5
C18 A:EM8202 4.3 16.5 0.5
C14 A:EM8202 4.3 16.8 0.5
CA A:LEU5 4.4 15.6 1.0
CB A:PRO17 4.5 20.5 1.0
C18 A:EM8202 4.5 17.6 0.5
CG2 A:ILE2 4.5 19.6 0.5
C A:ALA6 4.7 16.5 1.0
CD1 A:LEU5 4.7 16.0 1.0
C19 A:EM8202 4.7 16.6 0.5
C A:ILE2 4.8 18.1 1.0
C19 A:EM8202 4.8 17.7 0.5

Fluorine binding site 5 out of 12 in 6g5j

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Fluorine binding site 5 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.7
occ:0.50
 F29 A:EM8202 0.0 21.7 0.5
C26 A:EM8202 1.4 20.8 0.5
O25 A:EM8202 1.6 18.9 0.5
F27 A:EM8202 2.3 21.5 0.5
F28 A:EM8202 2.3 21.5 0.5
O25 A:EM8202 2.3 20.7 0.5
C16 A:EM8202 2.4 17.5 0.5
C26 A:EM8202 2.5 20.2 0.5
CG A:MET21 2.5 25.2 0.5
CG A:MET21 2.6 26.8 0.5
F29 A:EM8202 2.6 21.5 0.5
C15 A:EM8202 2.7 17.1 0.5
C16 A:EM8202 2.8 18.9 0.5
C15 A:EM8202 2.9 18.5 0.5
F27 A:EM8202 3.0 20.7 0.5
SD A:MET21 3.1 29.5 0.5
O A:PRO17 3.3 21.3 1.0
C17 A:EM8202 3.5 16.8 0.5
SD A:MET21 3.5 26.9 0.5
CB A:MET21 3.6 24.2 0.5
CA A:MET21 3.7 23.2 0.5
CA A:MET21 3.7 23.7 0.5
CB A:MET21 3.7 25.2 0.5
F28 A:EM8202 3.7 21.3 0.5
N A:MET21 3.8 22.2 1.0
C17 A:EM8202 3.9 18.3 0.5
C A:PRO17 4.0 20.2 1.0
C14 A:EM8202 4.0 16.8 0.5
C14 A:EM8202 4.1 18.0 0.5
C A:TYR20 4.2 20.2 1.0
CA A:ILE18 4.4 22.8 1.0
N A:ILE18 4.4 21.7 1.0
CE A:MET21 4.4 26.7 0.5
O A:TYR20 4.5 20.2 1.0
C10 A:EM8202 4.6 19.7 0.5
C18 A:EM8202 4.6 16.5 0.5
CE A:MET21 4.6 29.0 0.5
C10 A:EM8202 4.7 18.8 0.5
C A:ILE18 4.8 21.5 1.0
O A:ILE18 4.8 20.1 1.0
C19 A:EM8202 4.8 16.6 0.5
C18 A:EM8202 4.9 17.6 0.5
CB A:PRO17 4.9 20.5 1.0
C19 A:EM8202 4.9 17.7 0.5
CA A:TYR20 5.0 19.0 1.0
N13 A:EM8202 5.0 18.1 0.5
N A:TYR20 5.0 18.8 1.0

Fluorine binding site 6 out of 12 in 6g5j

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Fluorine binding site 6 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:21.5
occ:0.50
 F29 A:EM8202 0.0 21.5 0.5
F28 A:EM8202 0.5 21.5 0.5
C26 A:EM8202 1.4 20.2 0.5
C26 A:EM8202 1.9 20.8 0.5
F27 A:EM8202 2.3 20.7 0.5
F28 A:EM8202 2.3 21.3 0.5
O25 A:EM8202 2.3 18.9 0.5
F29 A:EM8202 2.6 21.7 0.5
O25 A:EM8202 2.7 20.7 0.5
F27 A:EM8202 2.8 21.5 0.5
C15 A:EM8202 2.9 17.1 0.5
C15 A:EM8202 2.9 18.5 0.5
C16 A:EM8202 2.9 17.5 0.5
C16 A:EM8202 3.2 18.9 0.5
CG2 A:ILE2 3.8 19.6 0.5
SD A:MET21 3.9 29.5 0.5
C14 A:EM8202 4.1 16.8 0.5
C14 A:EM8202 4.2 18.0 0.5
C17 A:EM8202 4.2 16.8 0.5
C10 A:EM8202 4.5 19.7 0.5
C17 A:EM8202 4.5 18.3 0.5
CD2 A:LEU5 4.6 16.4 1.0
CG A:MET21 4.6 26.8 0.5
C10 A:EM8202 4.6 18.8 0.5
CG A:MET21 4.6 25.2 0.5
CG1 A:ILE2 4.7 20.5 0.5
CB A:ILE2 4.7 18.9 0.5
O A:ILE2 4.8 19.0 1.0
C11 A:EM8202 4.8 19.2 0.5
CB A:ILE2 4.9 19.3 0.5
C11 A:EM8202 4.9 18.2 0.5
N13 A:EM8202 4.9 18.1 0.5
CG A:LEU5 5.0 15.8 1.0
N13 A:EM8202 5.0 17.1 0.5
C9 A:EM8202 5.0 19.7 0.5

Fluorine binding site 7 out of 12 in 6g5j

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Fluorine binding site 7 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:32.9
occ:0.50
 F27 A:EM8203 0.0 32.9 0.5
C26 A:EM8203 1.4 31.6 0.5
O25 A:EM8203 2.3 30.3 0.5
F29 A:EM8203 2.3 33.2 0.5
F28 A:EM8203 2.3 33.4 0.5
C16 A:EM8203 2.8 27.6 0.5
C17 A:EM8203 3.1 26.9 0.5
CG2 A:ILE18 3.6 26.4 1.0
C15 A:EM8203 3.8 26.0 0.5
C18 A:EM8203 4.2 25.3 0.5
CZ A:PHE109 4.4 28.9 1.0
C14 A:EM8203 4.7 24.5 0.5
C19 A:EM8203 4.9 24.6 0.5

Fluorine binding site 8 out of 12 in 6g5j

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Fluorine binding site 8 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:33.4
occ:0.50
 F28 A:EM8203 0.0 33.4 0.5
C26 A:EM8203 1.4 31.6 0.5
F29 A:EM8203 2.3 33.2 0.5
F27 A:EM8203 2.3 32.9 0.5
O25 A:EM8203 2.3 30.3 0.5
C16 A:EM8203 2.8 27.6 0.5
C15 A:EM8203 2.9 26.0 0.5
C17 A:EM8203 3.9 26.9 0.5
CG2 A:ILE18 4.0 26.4 1.0
C14 A:EM8203 4.1 24.5 0.5
CD2 A:LEU108 4.3 21.8 1.0
C1 A:EM8203 4.5 23.9 0.5
CZ A:PHE109 4.5 28.9 1.0
CE2 A:PHE109 4.6 27.9 1.0
CD1 A:LEU108 4.7 21.3 1.0
C12 A:EM8203 4.7 23.2 0.5
C18 A:EM8203 4.8 25.3 0.5
C19 A:EM8203 4.9 24.6 0.5

Fluorine binding site 9 out of 12 in 6g5j

Go back to Fluorine Binding Sites List in 6g5j
Fluorine binding site 9 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:33.2
occ:0.50
 F29 A:EM8203 0.0 33.2 0.5
C26 A:EM8203 1.4 31.6 0.5
F28 A:EM8203 2.3 33.4 0.5
F27 A:EM8203 2.3 32.9 0.5
O25 A:EM8203 2.3 30.3 0.5
CZ A:PHE109 3.5 28.9 1.0
CE2 A:PHE109 3.5 27.9 1.0
C16 A:EM8203 3.5 27.6 0.5
C15 A:EM8203 4.3 26.0 0.5
C17 A:EM8203 4.4 26.9 0.5
CE1 A:PHE109 4.8 28.0 1.0
CD2 A:PHE109 4.9 27.4 1.0
CD2 A:LEU108 5.0 21.8 1.0

Fluorine binding site 10 out of 12 in 6g5j

Go back to Fluorine Binding Sites List in 6g5j
Fluorine binding site 10 out of 12 in the Secreted Phospholipase A2 Type X in Complex with Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Secreted Phospholipase A2 Type X in Complex with Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F202

b:27.8
occ:1.00
 F27 B:EM8202 0.0 27.8 1.0
C26 B:EM8202 1.4 26.7 1.0
F28 B:EM8202 2.2 28.0 1.0
F29 B:EM8202 2.3 29.5 1.0
O25 B:EM8202 2.3 25.8 1.0
CD1 B:ILE18 3.1 21.1 0.5
CG2 B:ILE18 3.4 19.3 0.5
C B:PRO17 3.6 18.8 1.0
C16 B:EM8202 3.6 22.0 1.0
O B:PRO17 3.6 18.9 1.0
CB B:PRO17 3.6 19.4 1.0
CB B:ALA6 3.7 18.0 1.0
N B:ILE18 3.7 19.0 1.0
CA B:ILE18 3.9 18.8 0.5
CA B:ILE18 4.0 19.4 0.5
CG1 B:ILE18 4.1 21.0 0.5
CG B:PRO17 4.3 19.4 1.0
CA B:PRO17 4.3 18.8 1.0
C15 B:EM8202 4.3 20.1 1.0
CB B:ILE18 4.3 19.1 0.5
CA B:ALA6 4.4 17.8 1.0
C17 B:EM8202 4.6 21.3 1.0
CB B:ILE18 4.8 20.6 0.5

Reference:

F.Giordanetto, L.Knerr, P.Nordberg, D.Pettersen, N.Selmi, H.G.Beisel, H.De La Motte, A.Mansson, M.Dahlstrom, J.Broddefalk, G.Saarinen, F.Klingegard, E.Hurt-Camejo, B.Rosengren, J.Wikstrom, M.Wagberg, J.Brengdahl, M.Rohman, J.Sandmark, T.Akerud, R.G.Roth, F.Jansen, M.Ahlqvist. Design of Selective SPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(Trifluoromethoxy) -1H-Indol-1-Yl]Pyridine-2-Yl}Propanoic Acid. Acs Med Chem Lett V. 9 600 2018.
ISSN: ISSN 1948-5875
PubMed: 30034586
DOI: 10.1021/ACSMEDCHEMLETT.7B00507
Page generated: Tue Jul 15 11:46:39 2025

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