Fluorine in PDB 8b92: Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2)

The structure of Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2), PDB code: 8b92 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)	49.26 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.257, 85.698, 120.399, 90, 90, 90
R / Rfree (%)	19.5 / 22.7

The binding sites of Fluorine atom in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2) (pdb code 8b92). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2), PDB code: 8b92:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2)


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 An Inverse Agonist (Compound Si-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:29.9 occ:1.00 F8 A:Q5X501 0.0 29.9 1.0 C7 A:Q5X501 1.3 24.7 1.0 C9 A:Q5X501 2.3 23.2 1.0 C6 A:Q5X501 2.4 26.5 1.0 N5 A:Q5X501 2.8 24.6 1.0 CA A:SER289 3.1 24.9 1.0 C4 A:Q5X501 3.1 27.9 1.0 O17 A:Q5X501 3.2 30.0 1.0 CG2 A:ILE326 3.2 23.4 1.0 CB A:SER289 3.3 26.0 1.0 CD1 A:ILE326 3.4 22.3 1.0 C16 A:Q5X501 3.6 27.6 1.0 C10 A:Q5X501 3.6 27.0 1.0 CG1 A:ILE326 3.7 21.6 1.0 N A:SER289 3.7 23.1 1.0 CB A:ALA292 3.9 21.8 1.0 CB A:ILE326 4.1 20.4 1.0 C15 A:Q5X501 4.1 26.2 1.0 C3 A:Q5X501 4.2 27.3 1.0 C A:ARG288 4.3 23.7 1.0 C18 A:Q5X501 4.3 32.6 1.0 O A:ARG288 4.3 26.2 1.0 C A:SER289 4.3 27.1 1.0 O A:SER289 4.5 23.3 1.0 OG A:SER289 4.7 27.0 1.0 O A:CYS285 4.8 28.5 1.0 C11 A:Q5X501 4.9 29.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2)


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 An Inverse Agonist (Compound Si-2) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:34.8 occ:1.00 F33 A:Q5X501 0.0 34.8 1.0 C32 A:Q5X501 1.3 33.8 1.0 C34 A:Q5X501 2.3 28.2 1.0 C19 A:Q5X501 2.4 29.6 1.0 CZ A:PHE282 2.9 41.5 1.0 N21 A:Q5X501 2.9 33.0 1.0 C20 A:Q5X501 2.9 32.9 1.0 OE1 A:GLN286 3.1 37.4 1.0 CE1 A:PHE282 3.3 40.7 1.0 CE2 A:PHE282 3.6 44.2 1.0 C2 A:Q5X501 3.6 29.8 1.0 C18 A:Q5X501 3.6 32.6 1.0 CD2 A:LEU453 3.7 36.2 1.0 O31 A:Q5X501 4.0 29.3 1.0 CB A:GLN286 4.0 29.4 1.0 C3 A:Q5X501 4.1 27.3 1.0 C22 A:Q5X501 4.1 31.7 1.0 CA A:GLN286 4.1 29.3 1.0 CD A:GLN286 4.2 37.5 1.0 CZ A:PHE363 4.2 35.5 1.0 CD1 A:PHE282 4.3 41.0 1.0 N A:GLN286 4.4 31.2 1.0 CD2 A:PHE282 4.5 41.6 1.0 CG A:GLN286 4.7 33.2 1.0 O A:PHE282 4.7 33.2 1.0 CG A:PHE282 4.9 39.0 1.0 CE2 A:PHE363 4.9 38.6 1.0 CE1 A:PHE363 4.9 35.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2)


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 An Inverse Agonist (Compound Si-2) within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:48.6 occ:1.00 F8 B:Q5X501 0.0 48.6 1.0 C7 B:Q5X501 1.3 38.9 1.0 C6 B:Q5X501 2.4 38.8 1.0 C9 B:Q5X501 2.4 45.0 1.0 N5 B:Q5X501 2.7 32.7 1.0 C4 B:Q5X501 3.0 31.7 1.0 O17 B:Q5X501 3.0 33.9 1.0 CG2 B:ILE326 3.1 22.2 1.0 CA B:SER289 3.3 27.8 1.0 CB B:SER289 3.4 26.1 1.0 CD1 B:ILE326 3.5 21.6 1.0 C16 B:Q5X501 3.6 45.6 1.0 C10 B:Q5X501 3.7 44.7 1.0 CG1 B:ILE326 3.9 22.6 1.0 N B:SER289 4.0 29.8 1.0 CB B:ILE326 4.0 20.2 1.0 C3 B:Q5X501 4.1 27.3 1.0 CB B:ALA292 4.1 27.4 1.0 C15 B:Q5X501 4.1 44.2 1.0 C18 B:Q5X501 4.2 30.3 1.0 C B:ARG288 4.5 30.6 1.0 O B:ARG288 4.5 29.9 1.0 C B:SER289 4.6 27.2 1.0 O B:SER289 4.7 27.5 1.0 OG B:SER289 4.8 29.1 1.0 C11 B:Q5X501 4.9 50.0 1.0 O B:CYS285 4.9 28.2 1.0 OH B:TYR327 5.0 28.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Pparg and NCOR2 with An Inverse Agonist (Compound Si-2)


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 An Inverse Agonist (Compound Si-2) within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:30.0 occ:1.00 F33 B:Q5X501 0.0 30.0 1.0 C32 B:Q5X501 1.4 29.8 1.0 C19 B:Q5X501 2.4 27.6 1.0 C34 B:Q5X501 2.4 29.4 1.0 OE1 B:GLN286 2.6 41.2 1.0 N21 B:Q5X501 2.7 28.6 1.0 C20 B:Q5X501 2.8 28.4 1.0 O B:HOH650 3.2 61.4 1.0 CZ B:PHE282 3.4 34.3 1.0 CE1 B:PHE282 3.5 32.9 1.0 CD2 B:LEU453 3.6 29.4 1.0 C18 B:Q5X501 3.7 30.3 1.0 C2 B:Q5X501 3.7 28.4 1.0 CD B:GLN286 3.8 40.5 1.0 O31 B:Q5X501 3.9 28.0 1.0 C22 B:Q5X501 3.9 29.0 1.0 CB B:GLN286 4.1 32.0 1.0 C3 B:Q5X501 4.1 27.3 1.0 CA B:GLN286 4.2 31.6 1.0 CE2 B:PHE282 4.2 35.7 1.0 CZ B:PHE363 4.3 38.5 1.0 CD1 B:PHE282 4.5 32.8 1.0 CG B:GLN286 4.5 35.4 1.0 N B:GLN286 4.6 31.3 1.0 NE2 B:GLN286 4.8 42.2 1.0 C23 B:Q5X501 4.9 33.1 1.0 O B:PHE282 4.9 28.6 1.0 CG B:LEU453 5.0 30.0 1.0 CE2 B:PHE363 5.0 40.5 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