Fluorine in PDB 8b94: Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist

The structure of Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist, PDB code: 8b94 was solved by A.Friberg, D.L.Orsi, E.Pook, S.Siegel, C.T.Lemke, T.Stellfeld, V.Puetter, J.Goldstein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.10 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.444, 85.896, 121.271, 90, 90, 90
R / Rfree (%)	21.2 / 24

The binding sites of Fluorine atom in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist (pdb code 8b94). 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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist, PDB code: 8b94:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:34.3 occ:1.00 F1 A:Q5O501 0.0 34.3 1.0 C6 A:Q5O501 1.3 37.5 1.0 C1 A:Q5O501 2.4 35.0 1.0 C5 A:Q5O501 2.4 31.3 1.0 N2 A:Q5O501 2.7 37.5 1.0 C16 A:Q5O501 2.8 39.1 1.0 OE1 A:GLN286 3.2 62.5 1.0 CZ A:PHE282 3.2 39.4 1.0 CE1 A:PHE282 3.4 36.2 1.0 CD2 A:LEU453 3.6 39.7 1.0 C2 A:Q5O501 3.6 32.5 1.0 C4 A:Q5O501 3.6 33.0 1.0 O3 A:Q5O501 3.9 33.7 1.0 C17 A:Q5O501 4.1 37.3 1.0 CE2 A:PHE282 4.1 36.7 1.0 CA A:GLN286 4.1 33.2 1.0 CB A:GLN286 4.1 39.0 1.0 C3 A:Q5O501 4.1 31.5 1.0 CZ A:PHE363 4.2 37.2 1.0 CD A:GLN286 4.3 55.4 1.0 CD1 A:PHE282 4.4 38.8 1.0 N A:GLN286 4.4 32.7 1.0 CE1 A:PHE363 4.7 37.5 1.0 CG A:GLN286 4.8 50.3 1.0 O A:PHE282 4.8 33.4 1.0 CG A:LEU453 4.9 39.2 1.0 CD2 A:PHE282 4.9 34.5 1.0 C A:CYS285 4.9 31.2 1.0 CD1 A:LEU453 5.0 42.1 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:52.9 occ:1.00 F2 A:Q5O501 0.0 52.9 1.0 C15 A:Q5O501 1.3 47.5 1.0 O1 A:Q5O501 2.2 34.4 1.0 F3 A:Q5O501 2.2 49.8 1.0 O A:HOH793 2.7 36.2 1.0 C11 A:Q5O501 2.9 29.8 1.0 C10 A:Q5O501 3.0 27.8 1.0 NH1 A:ARG288 3.8 42.6 1.0 CB A:ALA292 3.8 28.2 1.0 CB A:MET329 3.9 29.6 1.0 C12 A:Q5O501 4.2 29.2 1.0 O A:ILE326 4.3 22.4 0.4 C9 A:Q5O501 4.3 31.3 1.0 CZ A:ARG288 4.4 37.6 1.0 CA A:ILE326 4.6 23.1 0.4 O A:HOH703 4.6 36.4 1.0 CG2 A:ILE326 4.7 23.1 0.4 SD A:MET329 4.7 37.4 1.0 CG1 A:ILE326 4.7 26.9 0.6 C A:MET329 4.8 24.3 1.0 CG A:MET329 4.8 33.8 1.0 N A:LEU330 4.8 22.2 1.0 NH2 A:ARG288 4.8 42.8 1.0 CG1 A:ILE326 4.9 24.6 0.4 O A:ILE326 4.9 20.7 0.6 C A:ILE326 4.9 20.9 0.4 CA A:ILE326 4.9 22.2 0.6 NE A:ARG288 4.9 35.9 1.0 CA A:MET329 4.9 24.9 1.0 CB A:ILE326 4.9 22.8 0.4 CA A:ALA292 5.0 27.4 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:49.8 occ:1.00 F3 A:Q5O501 0.0 49.8 1.0 C15 A:Q5O501 1.4 47.5 1.0 O1 A:Q5O501 2.1 34.4 1.0 F2 A:Q5O501 2.2 52.9 1.0 C11 A:Q5O501 3.0 29.8 1.0 N A:LEU330 3.0 22.2 1.0 C A:MET329 3.1 24.3 1.0 CA A:LEU330 3.4 24.2 1.0 CB A:MET329 3.5 29.6 1.0 O A:ILE326 3.5 22.4 0.4 O A:MET329 3.5 23.9 1.0 C10 A:Q5O501 3.7 27.8 1.0 O A:HOH703 3.7 36.4 1.0 CD1 A:LEU330 3.8 34.2 1.0 CA A:MET329 3.9 24.9 1.0 C12 A:Q5O501 3.9 29.2 1.0 O A:ILE326 4.0 20.7 0.6 CB A:LEU330 4.0 26.4 1.0 CD1 A:LEU333 4.1 27.4 1.0 O A:HOH793 4.2 36.2 1.0 CG A:LEU330 4.4 37.8 1.0 C A:ILE326 4.6 20.9 0.4 CG A:LEU333 4.7 24.9 1.0 C A:LEU330 4.7 22.0 1.0 N A:MET329 4.7 23.3 1.0 CG2 A:ILE326 4.9 23.1 0.4 CG A:MET329 4.9 33.8 1.0 C9 A:Q5O501 4.9 31.3 1.0 CA A:ILE326 4.9 23.1 0.4 C A:ILE326 5.0 20.8 0.6

Fluorine binding site 4 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:52.0 occ:1.00 F4 A:Q5O501 0.0 52.0 1.0 C21 A:Q5O501 1.4 44.3 1.0 C20 A:Q5O501 2.4 44.2 1.0 C22 A:Q5O501 2.4 42.0 1.0 CD1 C:ILE2353 2.9 49.3 1.0 C19 A:Q5O501 3.6 40.4 1.0 C23 A:Q5O501 3.7 41.7 1.0 CD1 C:LEU2350 3.7 44.5 1.0 CA C:LEU2350 3.7 40.2 1.0 CG2 A:VAL290 3.8 31.0 1.0 N C:LEU2350 4.1 42.7 1.0 C18 A:Q5O501 4.1 40.2 1.0 CG1 C:ILE2353 4.2 43.4 1.0 CB C:LEU2350 4.3 41.9 1.0 C C:GLY2349 4.4 42.2 1.0 CB C:ILE2353 4.4 42.3 1.0 CG2 A:VAL293 4.4 31.1 1.0 CA A:VAL290 4.5 28.4 1.0 O C:GLY2349 4.5 43.0 1.0 NE2 A:GLN286 4.6 57.9 1.0 CB A:VAL290 4.6 31.5 1.0 CG C:LEU2350 4.7 43.0 1.0 CG2 C:ILE2353 4.8 45.4 1.0 C C:LEU2350 4.9 40.7 1.0 CB A:VAL293 4.9 29.7 1.0 O C:LEU2350 4.9 38.0 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:34.5 occ:1.00 F1 B:Q5O501 0.0 34.5 1.0 C6 B:Q5O501 1.3 31.9 1.0 C1 B:Q5O501 2.3 31.6 1.0 C5 B:Q5O501 2.4 30.0 1.0 OE1 B:GLN286 2.5 60.0 1.0 N2 B:Q5O501 2.7 35.1 1.0 C16 B:Q5O501 2.8 31.9 1.0 CZ B:PHE282 3.2 38.1 1.0 CE1 B:PHE282 3.4 36.8 1.0 CD2 B:LEU453 3.5 30.6 1.0 C2 B:Q5O501 3.6 34.0 1.0 C4 B:Q5O501 3.7 33.7 1.0 CD B:GLN286 3.7 57.0 1.0 O3 B:Q5O501 3.9 31.0 1.0 C17 B:Q5O501 4.0 37.1 1.0 CB B:GLN286 4.1 40.1 1.0 CA B:GLN286 4.1 36.9 1.0 CE2 B:PHE282 4.1 40.1 1.0 C3 B:Q5O501 4.1 32.6 1.0 CZ B:PHE363 4.3 38.9 1.0 CD1 B:PHE282 4.4 35.1 1.0 N B:GLN286 4.5 35.6 1.0 CG B:GLN286 4.5 47.0 1.0 NE2 B:GLN286 4.6 61.6 1.0 CG B:LEU453 4.8 31.8 1.0 O B:PHE282 4.9 33.7 1.0 CD2 B:PHE282 5.0 36.1 1.0 C18 B:Q5O501 5.0 38.8 1.0 CD1 B:LEU453 5.0 35.4 1.0 OG B:SER289 5.0 28.8 0.6 CE1 B:PHE363 5.0 42.5 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.4 occ:1.00 F2 B:Q5O501 0.0 53.4 1.0 C15 B:Q5O501 1.4 50.2 1.0 F3 B:Q5O501 2.2 53.2 1.0 O1 B:Q5O501 2.4 45.7 1.0 O B:HOH737 2.9 42.0 1.0 C10 B:Q5O501 3.0 40.8 1.0 C11 B:Q5O501 3.1 43.3 1.0 CB B:ALA292 3.9 28.1 1.0 O B:ILE326 4.0 23.8 1.0 NH1 B:ARG288 4.0 44.8 1.0 CB B:MET329 4.1 25.3 1.0 CA B:ILE326 4.2 21.2 1.0 CG2 B:ILE326 4.2 24.1 1.0 C9 B:Q5O501 4.3 33.6 1.0 C12 B:Q5O501 4.4 38.7 1.0 N B:LEU330 4.5 23.2 1.0 CB B:ILE326 4.6 22.8 1.0 C B:ILE326 4.6 22.8 1.0 CG1 B:ILE326 4.6 26.3 1.0 CZ B:ARG288 4.6 45.2 1.0 C B:MET329 4.8 21.4 1.0 O B:HOH711 4.9 44.4 1.0 SD B:MET329 5.0 33.2 1.0 CA B:LEU330 5.0 24.2 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:53.2 occ:1.00 F3 B:Q5O501 0.0 53.2 1.0 C15 B:Q5O501 1.4 50.2 1.0 O1 B:Q5O501 2.2 45.7 1.0 F2 B:Q5O501 2.2 53.4 1.0 N B:LEU330 3.2 23.2 1.0 CA B:LEU330 3.3 24.2 1.0 C11 B:Q5O501 3.3 43.3 1.0 C B:MET329 3.4 21.4 1.0 O B:MET329 3.6 24.5 1.0 O B:HOH711 3.7 44.4 1.0 CB B:LEU330 3.8 27.7 1.0 CB B:MET329 3.8 25.3 1.0 CD1 B:LEU333 4.0 31.1 1.0 C10 B:Q5O501 4.0 40.8 1.0 O B:ILE326 4.0 23.8 1.0 CD1 B:LEU330 4.0 30.1 1.0 CA B:MET329 4.2 22.3 1.0 C12 B:Q5O501 4.3 38.7 1.0 O B:HOH737 4.4 42.0 1.0 CG B:LEU333 4.5 30.1 1.0 CG B:LEU330 4.5 30.9 1.0 NH1 B:ARG288 4.6 44.8 1.0 C B:LEU330 4.6 25.2 1.0 O B:HOH613 4.7 50.8 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Pparg and NCOR2 with Bay-5516, An Inverse Agonist


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 Pparg and NCOR2 with Bay-5516, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:48.7 occ:1.00 F4 B:Q5O501 0.0 48.7 1.0 C21 B:Q5O501 1.4 46.5 1.0 C20 B:Q5O501 2.4 42.0 1.0 C22 B:Q5O501 2.4 44.8 1.0 CD1 D:ILE2353 3.1 49.1 1.0 CD1 D:LEU2350 3.6 45.6 1.0 C19 B:Q5O501 3.6 37.7 1.0 C23 B:Q5O501 3.7 43.4 1.0 CG2 B:VAL290 3.8 39.1 1.0 CG2 B:VAL293 4.0 29.5 1.0 CA D:LEU2350 4.1 43.4 1.0 C18 B:Q5O501 4.2 38.8 1.0 CA B:VAL290 4.3 32.2 1.0 CG1 D:ILE2353 4.3 47.0 1.0 CB D:ILE2353 4.3 41.7 1.0 CG2 D:ILE2353 4.3 43.0 1.0 CB B:VAL293 4.5 26.3 1.0 CB D:LEU2350 4.5 45.5 1.0 CB B:VAL290 4.5 34.6 1.0 CG D:LEU2350 4.7 45.5 1.0 CG1 B:VAL293 4.7 29.5 1.0 N D:LEU2350 4.7 47.5 1.0 N B:VAL290 4.8 29.2 1.0 CG1 B:VAL290 4.9 35.1 1.0 NE2 B:GLN286 4.9 61.6 1.0 O B:SER289 5.0 28.9 0.4

D.L.Orsi, S.J.Ferrara, S.Siegel, A.Friberg, L.Bouche, E.Pook, P.Lienau, J.P.Bluck, C.T.Lemke, G.Akcay, T.Stellfeld, H.Meyer, V.Putter, S.J.Holton, D.Korr, I.Jerchel-Furau, C.Pantelidou, C.A.Strathdee, M.Meyerson, K.Eis, J.T.Goldstein. Discovery and Characterization of Orally Bioavailable 4-Chloro-6-Fluoroisophthalamides As Covalent Pparg Inverse-Agonists. Bioorg.Med.Chem. V. 78 17130 2022.
ISSN: ESSN 1464-3391
PubMed: 36542958
DOI: 10.1016/J.BMC.2022.117130