Fluorine in PDB 8b95: Crystal Structure of Pparg and NCOR2 with Bay-9683, An Inverse Agonist

The structure of Crystal Structure of Pparg and NCOR2 with Bay-9683, An Inverse Agonist, PDB code: 8b95 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)	42.83 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.643, 86.066, 121.009, 90, 90, 90
R / Rfree (%)	19.6 / 23.8

The binding sites of Fluorine atom in the Crystal Structure of Pparg and NCOR2 with Bay-9683, An Inverse Agonist (pdb code 8b95). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Pparg and NCOR2 with Bay-9683, An Inverse Agonist, PDB code: 8b95:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:63.6 occ:1.00 F1 A:Q4C501 0.0 63.6 1.0 C7 A:Q4C501 1.3 54.0 1.0 C8 A:Q4C501 2.3 52.9 1.0 C6 A:Q4C501 2.4 49.6 1.0 F2 A:Q4C501 2.7 55.5 1.0 CG2 A:VAL293 3.1 50.5 1.0 O A:SER289 3.4 35.9 1.0 C A:SER289 3.5 35.6 1.0 C9 A:Q4C501 3.6 53.2 1.0 OG A:SER289 3.6 42.0 1.0 CD1 C:LEU2350 3.6 67.5 1.0 N A:VAL290 3.6 38.6 1.0 C5 A:Q4C501 3.6 46.2 1.0 CA A:VAL290 3.7 38.8 1.0 CG2 A:VAL290 3.9 36.8 1.0 C10 A:Q4C501 4.1 52.8 1.0 CB A:SER289 4.1 37.3 1.0 CB A:VAL293 4.2 46.8 1.0 CA A:SER289 4.4 32.5 1.0 CB A:VAL290 4.4 37.6 1.0 C A:VAL290 4.8 37.3 1.0 O A:VAL290 4.9 42.2 1.0 CG C:LEU2350 4.9 62.5 1.0 NE2 A:GLN286 4.9 61.0 1.0 C4 A:Q4C501 4.9 42.2 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:55.5 occ:1.00 F2 A:Q4C501 0.0 55.5 1.0 C8 A:Q4C501 1.3 52.9 1.0 C9 A:Q4C501 2.4 53.2 1.0 C7 A:Q4C501 2.4 54.0 1.0 F1 A:Q4C501 2.7 63.6 1.0 CD1 C:ILE2353 3.1 65.0 1.0 CD1 C:LEU2350 3.5 67.5 1.0 C10 A:Q4C501 3.6 52.8 1.0 C6 A:Q4C501 3.6 49.6 1.0 CA C:LEU2350 3.8 58.0 1.0 CG2 A:VAL290 3.8 36.8 1.0 N C:LEU2350 3.9 63.0 1.0 C5 A:Q4C501 4.1 46.2 1.0 C C:GLY2349 4.3 68.0 1.0 CB C:LEU2350 4.4 64.1 1.0 CG1 C:ILE2353 4.5 61.5 1.0 O C:GLY2349 4.5 64.8 1.0 CG C:LEU2350 4.5 62.5 1.0 CG2 A:VAL293 4.7 50.5 1.0 CA A:VAL290 4.7 38.8 1.0 CB A:VAL290 4.7 37.6 1.0 NE2 A:GLN286 4.7 61.0 1.0 CD1 A:LEU469 4.8 79.0 1.0 CB C:ILE2353 4.9 58.8 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:42.3 occ:1.00 F3 A:Q4C501 0.0 42.3 1.0 C1 A:Q4C501 1.3 41.5 1.0 C2 A:Q4C501 2.4 40.3 1.0 C20 A:Q4C501 2.4 38.0 1.0 N1 A:Q4C501 2.7 42.9 1.0 C3 A:Q4C501 2.8 44.8 1.0 OE1 A:GLN286 2.9 62.2 1.0 CZ A:PHE282 3.2 52.4 1.0 CE1 A:PHE282 3.5 46.0 1.0 CD2 A:LEU453 3.6 48.6 1.0 C11 A:Q4C501 3.6 37.8 1.0 C19 A:Q4C501 3.7 38.3 1.0 O1 A:Q4C501 3.9 40.3 1.0 CE2 A:PHE282 3.9 51.7 1.0 C4 A:Q4C501 4.0 42.2 1.0 CD A:GLN286 4.0 62.9 1.0 CA A:GLN286 4.0 41.7 1.0 CB A:GLN286 4.0 45.2 1.0 C12 A:Q4C501 4.1 35.8 1.0 CZ A:PHE363 4.1 45.0 1.0 N A:GLN286 4.3 39.2 1.0 CD1 A:PHE282 4.4 46.2 1.0 CG A:GLN286 4.6 54.6 1.0 CD2 A:PHE282 4.7 51.3 1.0 O A:PHE282 4.8 38.2 1.0 CE2 A:PHE363 4.8 50.0 1.0 CE1 A:PHE363 4.9 49.2 1.0 CG A:LEU453 4.9 48.0 1.0 C A:CYS285 5.0 39.7 1.0 CG A:PHE282 5.0 41.9 1.0 OG A:SER289 5.0 42.0 1.0 C5 A:Q4C501 5.0 46.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:62.8 occ:1.00 F1 B:Q4C501 0.0 62.8 1.0 C7 B:Q4C501 1.3 57.7 1.0 C8 B:Q4C501 2.3 59.9 1.0 C6 B:Q4C501 2.4 47.8 1.0 F2 B:Q4C501 2.7 70.9 1.0 CG2 B:VAL293 3.2 42.9 1.0 O B:SER289 3.3 32.6 1.0 OG B:SER289 3.3 40.4 1.0 C B:SER289 3.4 34.8 1.0 N B:VAL290 3.5 37.5 1.0 C9 B:Q4C501 3.6 56.8 1.0 C5 B:Q4C501 3.6 47.6 1.0 CA B:VAL290 3.7 38.5 1.0 CB B:SER289 3.8 33.5 1.0 CG2 B:VAL290 4.0 42.6 1.0 CD1 D:LEU2350 4.1 53.2 1.0 C10 B:Q4C501 4.1 54.2 1.0 CA B:SER289 4.2 33.2 1.0 CB B:VAL293 4.3 41.2 1.0 CB B:VAL290 4.5 42.6 1.0 NE2 B:GLN286 4.7 72.7 1.0 C B:VAL290 4.9 35.8 1.0 C4 B:Q4C501 4.9 38.8 1.0 O B:GLN286 5.0 37.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:70.9 occ:1.00 F2 B:Q4C501 0.0 70.9 1.0 C8 B:Q4C501 1.3 59.9 1.0 C7 B:Q4C501 2.4 57.7 1.0 C9 B:Q4C501 2.4 56.8 1.0 F1 B:Q4C501 2.7 62.8 1.0 CD1 D:ILE2353 3.2 58.4 1.0 CD1 D:LEU2350 3.3 53.2 1.0 C10 B:Q4C501 3.6 54.2 1.0 C6 B:Q4C501 3.6 47.8 1.0 CA D:LEU2350 3.7 51.2 1.0 CG2 B:VAL290 3.9 42.6 1.0 N D:LEU2350 4.1 57.7 1.0 C5 B:Q4C501 4.1 47.6 1.0 CB D:LEU2350 4.2 54.0 1.0 CG D:LEU2350 4.4 50.9 1.0 CG2 B:VAL293 4.4 42.9 1.0 CG1 D:ILE2353 4.5 55.3 1.0 CA B:VAL290 4.6 38.5 1.0 CB D:ILE2353 4.7 49.6 1.0 C D:GLY2349 4.7 53.5 1.0 CB B:VAL290 4.7 42.6 1.0 CG2 D:ILE2353 4.9 52.7 1.0 C D:LEU2350 4.9 53.9 1.0 CB B:VAL293 5.0 41.2 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Pparg and NCOR2 with Bay-9683, 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-9683, An Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:37.0 occ:1.00 F3 B:Q4C501 0.0 37.0 1.0 C1 B:Q4C501 1.3 36.6 1.0 C2 B:Q4C501 2.3 36.2 1.0 C20 B:Q4C501 2.4 39.0 1.0 N1 B:Q4C501 2.8 38.1 1.0 C3 B:Q4C501 2.8 38.8 1.0 OE1 B:GLN286 2.8 61.0 1.0 CZ B:PHE282 3.1 43.4 1.0 CE1 B:PHE282 3.2 38.9 1.0 CD B:GLN286 3.5 58.8 1.0 CD2 B:LEU453 3.5 40.1 1.0 C11 B:Q4C501 3.6 36.5 1.0 C19 B:Q4C501 3.6 38.0 1.0 O1 B:Q4C501 3.9 38.5 1.0 CE2 B:PHE282 4.0 46.1 1.0 NE2 B:GLN286 4.0 72.7 1.0 C4 B:Q4C501 4.1 38.8 1.0 C12 B:Q4C501 4.1 34.5 1.0 CZ B:PHE363 4.1 47.2 1.0 CB B:GLN286 4.2 43.2 1.0 CD1 B:PHE282 4.2 41.0 1.0 CA B:GLN286 4.2 40.4 1.0 CG B:GLN286 4.4 52.6 1.0 N B:GLN286 4.5 42.0 1.0 CD2 B:PHE282 4.8 43.6 1.0 O B:PHE282 4.8 36.0 1.0 CE1 B:PHE363 4.8 52.7 1.0 CG B:LEU453 4.9 37.8 1.0 CE2 B:PHE363 4.9 46.7 1.0 CG B:PHE282 4.9 40.2 1.0

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