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Fluorine in PDB 5ow8: Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors

Enzymatic activity of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors

All present enzymatic activity of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors:
3.1.1.4;

Protein crystallography data

The structure of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors, PDB code: 5ow8 was solved by J.S.Sandmark, R.G.Roth, L.Knerr, C.Bodin, D.Pettersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 27.652, 85.367, 102.954, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 25.2

Other elements in 5ow8:

The structure of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors (pdb code 5ow8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors, PDB code: 5ow8:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5ow8

Go back to Fluorine Binding Sites List in 5ow8
Fluorine binding site 1 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:27.4
occ:1.00
 F20 A:AYN206 0.0 27.4 1.0
C19 A:AYN206 1.4 26.4 1.0
F22 A:AYN206 2.3 27.1 1.0
F21 A:AYN206 2.3 27.5 1.0
C15 A:AYN206 2.4 25.4 1.0
C16 A:AYN206 2.8 24.6 1.0
CD1 A:ILE2 3.3 19.1 0.5
CD A:LYS61 3.4 23.4 1.0
C14 A:AYN206 3.6 24.0 1.0
CG A:LYS61 3.8 22.4 1.0
CD1 A:LEU29 3.8 21.4 1.0
CG2 A:ILE2 3.9 19.1 0.5
CG1 A:ILE2 4.1 19.0 0.5
C17 A:AYN206 4.2 24.2 1.0
CB A:LYS61 4.6 21.5 1.0
C13 A:AYN206 4.7 23.2 1.0
CE A:LYS61 4.9 24.3 1.0
C18 A:AYN206 5.0 23.5 1.0

Fluorine binding site 2 out of 6 in 5ow8

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Fluorine binding site 2 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:27.5
occ:1.00
 F21 A:AYN206 0.0 27.5 1.0
C19 A:AYN206 1.4 26.4 1.0
F20 A:AYN206 2.3 27.4 1.0
F22 A:AYN206 2.3 27.1 1.0
C15 A:AYN206 2.3 25.4 1.0
C16 A:AYN206 3.1 24.6 1.0
C14 A:AYN206 3.2 24.0 1.0
CD1 A:LEU29 3.3 21.4 1.0
O A:DMS203 3.4 27.4 1.0
C1 A:DMS203 3.4 28.3 1.0
C2 A:DMS203 3.4 28.6 1.0
S A:DMS203 3.6 28.4 1.0
CA A:LEU29 3.9 20.3 1.0
CD A:LYS61 4.1 23.4 1.0
C17 A:AYN206 4.4 24.2 1.0
C13 A:AYN206 4.4 23.2 1.0
CG A:LEU29 4.4 21.2 1.0
CB A:LEU29 4.4 20.7 1.0
N A:GLY30 4.5 20.2 1.0
CG A:LYS61 4.6 22.4 1.0
O A:GLY28 4.6 19.4 1.0
N A:LEU29 4.6 19.8 1.0
C A:LEU29 4.8 20.2 1.0
C A:GLY28 4.8 19.5 1.0
O11 A:AYN206 4.9 20.5 1.0
C18 A:AYN206 4.9 23.5 1.0

Fluorine binding site 3 out of 6 in 5ow8

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Fluorine binding site 3 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F206

b:27.1
occ:1.00
 F22 A:AYN206 0.0 27.1 1.0
C19 A:AYN206 1.4 26.4 1.0
F20 A:AYN206 2.3 27.4 1.0
F21 A:AYN206 2.3 27.5 1.0
C15 A:AYN206 2.4 25.4 1.0
C14 A:AYN206 2.7 24.0 1.0
CD1 A:ILE2 3.3 19.1 0.5
CE2 A:TYR50 3.6 17.6 1.0
C16 A:AYN206 3.7 24.6 1.0
C1 A:DMS203 3.7 28.3 1.0
CG A:LYS61 3.9 22.4 1.0
CD2 A:TYR50 3.9 18.0 1.0
C13 A:AYN206 4.1 23.2 1.0
CD A:LYS61 4.2 23.4 1.0
CD2 A:LEU5 4.3 16.6 1.0
CG2 A:ILE2 4.3 19.1 0.5
CG1 A:ILE2 4.6 19.0 0.5
CZ A:TYR50 4.7 17.3 1.0
C17 A:AYN206 4.8 24.2 1.0
S A:DMS203 4.8 28.4 1.0
C2 A:DMS203 4.8 28.6 1.0
CB A:LYS61 4.9 21.5 1.0
N7 A:AYN206 4.9 21.8 1.0
O A:DMS203 4.9 27.4 1.0
C18 A:AYN206 5.0 23.5 1.0

Fluorine binding site 4 out of 6 in 5ow8

Go back to Fluorine Binding Sites List in 5ow8
Fluorine binding site 4 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F206

b:28.1
occ:1.00
 F20 B:AYN206 0.0 28.1 1.0
C19 B:AYN206 1.4 26.8 1.0
F21 B:AYN206 2.3 28.1 1.0
F22 B:AYN206 2.3 27.8 1.0
C15 B:AYN206 2.4 25.7 1.0
C16 B:AYN206 2.8 24.7 1.0
CD1 B:ILE2 3.1 22.0 0.5
O B:DMS205 3.5 50.2 1.0
C14 B:AYN206 3.6 24.5 1.0
CG B:LYS61 3.8 23.6 1.0
S B:DMS205 4.0 50.0 1.0
C2 B:DMS205 4.1 48.8 1.0
CG1 B:ILE2 4.1 21.6 0.5
C17 B:AYN206 4.2 24.4 1.0
CD B:LYS61 4.4 24.8 1.0
CG B:LEU29 4.6 25.9 1.0
CD1 B:ILE2 4.6 21.8 0.5
C13 B:AYN206 4.8 23.6 1.0
CB B:LYS61 4.9 22.8 1.0
C18 B:AYN206 5.0 24.0 1.0

Fluorine binding site 5 out of 6 in 5ow8

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Fluorine binding site 5 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F206

b:28.1
occ:1.00
 F21 B:AYN206 0.0 28.1 1.0
C19 B:AYN206 1.4 26.8 1.0
F20 B:AYN206 2.3 28.1 1.0
F22 B:AYN206 2.3 27.8 1.0
C15 B:AYN206 2.3 25.7 1.0
C16 B:AYN206 3.2 24.7 1.0
C14 B:AYN206 3.2 24.5 1.0
O B:DMS202 3.4 27.5 1.0
C2 B:DMS202 3.5 28.1 1.0
C1 B:DMS202 3.5 27.8 1.0
S B:DMS202 3.7 27.9 1.0
CA B:LEU29 4.0 23.3 1.0
C17 B:AYN206 4.4 24.4 1.0
CG B:LEU29 4.4 25.9 1.0
C13 B:AYN206 4.4 23.6 1.0
O B:GLY28 4.5 20.9 1.0
N B:GLY30 4.5 22.1 1.0
CG B:LYS61 4.5 23.6 1.0
N B:LEU29 4.6 22.1 1.0
CD B:LYS61 4.7 24.8 1.0
CB B:LEU29 4.7 24.8 1.0
C B:GLY28 4.8 21.2 1.0
C B:LEU29 4.8 22.8 1.0
C18 B:AYN206 4.9 24.0 1.0
O11 B:AYN206 4.9 20.2 1.0
CD2 B:LEU29 5.0 26.6 1.0

Fluorine binding site 6 out of 6 in 5ow8

Go back to Fluorine Binding Sites List in 5ow8
Fluorine binding site 6 out of 6 in the Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Indole-2 Carboxamides As Selective Secreted Phospholipase A2 Type X (SPLA2-X) Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F206

b:27.8
occ:1.00
 F22 B:AYN206 0.0 27.8 1.0
C19 B:AYN206 1.4 26.8 1.0
F21 B:AYN206 2.3 28.1 1.0
F20 B:AYN206 2.3 28.1 1.0
C15 B:AYN206 2.4 25.7 1.0
C14 B:AYN206 2.8 24.5 1.0
C16 B:AYN206 3.7 24.7 1.0
CE2 B:TYR50 3.7 17.5 1.0
C1 B:DMS202 3.9 27.8 1.0
CG B:LYS61 3.9 23.6 1.0
CD2 B:TYR50 4.1 17.8 1.0
CD1 B:ILE2 4.1 22.0 0.5
C13 B:AYN206 4.1 23.6 1.0
CD2 B:LEU5 4.2 16.2 1.0
CG1 B:ILE2 4.4 21.6 0.5
C17 B:AYN206 4.8 24.4 1.0
CD B:LYS61 4.8 24.8 1.0
CZ B:TYR50 4.8 17.4 1.0
O B:DMS202 4.9 27.5 1.0
N7 B:AYN206 5.0 22.5 1.0
S B:DMS202 5.0 27.9 1.0
C18 B:AYN206 5.0 24.0 1.0
C2 B:DMS202 5.0 28.1 1.0

Reference:

L.Knerr, F.Giordanetto, P.Nordberg, D.Pettersen, N.Selmi, H.G.Beisel, H.De La Motte, T.Olsson, T.D.J.Perkins, M.Herslof, A.Mansson, M.Dahlstrom, I.Starke, J.Broddefalk, G.Saarinen, F.Klingegard, E.Hurt-Camejo, B.Rosengren, J.Brengdahl, F.Jansen, M.Rohman, J.Sandmark, K.Hallberg, T.Akerud, R.G.Roth, M.Ahlqvist. Discovery of A Series of Indole-2 Carboxamides As Selective Secreted Phospholipase A2TYPE X (SPLA2-X) Inhibitors. Acs Med Chem Lett V. 9 594 2018.
ISSN: ISSN 1948-5875
PubMed: 30034585
DOI: 10.1021/ACSMEDCHEMLETT.7B00505
Page generated: Thu Aug 1 12:37:10 2024

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