Fluorine in PDB 6sjm: Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)

The structure of Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175), PDB code: 6sjm was solved by A.Chaikuad, J.Pollinger, C.H.Arrowsmith, A.M.Edwards, C.Bountra, D.Merk, S.Knapp, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.25 / 2.52
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	63.998, 63.998, 109.596, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.7

The binding sites of Fluorine atom in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) (pdb code 6sjm). 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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175), PDB code: 6sjm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:84.5 occ:1.00 F5 A:LFZ501 0.0 84.5 1.0 C14 A:LFZ501 1.3 79.5 1.0 F3 A:LFZ501 2.1 89.8 1.0 F4 A:LFZ501 2.1 78.3 1.0 C13 A:LFZ501 2.3 78.7 1.0 C12 A:LFZ501 2.8 78.1 1.0 CA A:PHE346 3.5 62.4 1.0 C15 A:LFZ501 3.5 80.8 1.0 N A:PHE346 3.6 59.1 1.0 CG2 A:ILE345 3.6 61.2 1.0 CD1 A:PHE346 3.8 69.1 1.0 C A:ILE345 3.9 58.7 1.0 O A:ILE345 4.0 58.0 1.0 CG2 A:VAL349 4.1 57.3 1.0 CB A:PHE346 4.1 63.6 1.0 C10 A:LFZ501 4.1 85.0 1.0 CG1 A:ILE345 4.2 58.0 1.0 CG A:PHE346 4.3 68.0 1.0 CB A:ILE345 4.4 56.3 1.0 C8 A:LFZ501 4.6 82.9 1.0 CB A:VAL349 4.7 58.9 1.0 C A:PHE346 4.7 63.2 1.0 O A:VAL342 4.7 60.1 1.0 CA A:ILE345 4.8 58.7 1.0 CE1 A:PHE346 4.8 71.0 1.0 SG A:CYS432 4.8 64.9 1.0 O A:PHE346 4.9 62.0 1.0 C9 A:LFZ501 4.9 84.4 1.0 F2 A:LFZ501 5.0 83.4 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:89.8 occ:1.00 F3 A:LFZ501 0.0 89.8 1.0 C14 A:LFZ501 1.3 79.5 1.0 F5 A:LFZ501 2.1 84.5 1.0 F4 A:LFZ501 2.1 78.3 1.0 C13 A:LFZ501 2.3 78.7 1.0 CD1 A:PHE346 2.8 69.1 1.0 C12 A:LFZ501 3.0 78.1 1.0 C15 A:LFZ501 3.3 80.8 1.0 CE1 A:PHE346 3.5 71.0 1.0 CD1 A:ILE268 3.8 77.0 1.0 CG A:PHE346 3.9 68.0 1.0 CB A:PHE346 4.1 63.6 1.0 CA A:PHE346 4.2 62.4 1.0 C10 A:LFZ501 4.3 85.0 1.0 CG2 A:VAL342 4.5 60.4 1.0 C8 A:LFZ501 4.5 82.9 1.0 CD1 A:ILE324 4.5 73.9 1.0 N A:PHE346 4.7 59.1 1.0 O A:VAL342 4.8 60.1 1.0 CG2 A:ILE345 4.8 61.2 1.0 CG1 A:ILE268 4.8 77.3 1.0 CZ A:PHE346 4.9 73.7 1.0 C9 A:LFZ501 4.9 84.4 1.0 CB A:ALA337 4.9 68.6 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:78.3 occ:1.00 F4 A:LFZ501 0.0 78.3 1.0 C14 A:LFZ501 1.3 79.5 1.0 F5 A:LFZ501 2.1 84.5 1.0 F3 A:LFZ501 2.1 89.8 1.0 C13 A:LFZ501 2.3 78.7 1.0 C15 A:LFZ501 2.7 80.8 1.0 CD1 A:PHE346 3.5 69.1 1.0 CD1 A:ILE324 3.6 73.9 1.0 C12 A:LFZ501 3.6 78.1 1.0 CZ A:PHE313 3.8 67.4 1.0 CE1 A:PHE346 3.8 71.0 1.0 CE1 A:PHE313 3.9 68.9 1.0 C8 A:LFZ501 4.1 82.9 1.0 CG2 A:VAL349 4.2 57.3 1.0 CG A:PHE346 4.4 68.0 1.0 CA A:PHE346 4.5 62.4 1.0 CB A:VAL349 4.5 58.9 1.0 CG1 A:VAL349 4.6 62.0 1.0 CG1 A:ILE324 4.6 72.4 1.0 CG2 A:ILE324 4.6 70.2 1.0 C10 A:LFZ501 4.7 85.0 1.0 CB A:PHE346 4.8 63.6 1.0 CE2 A:PHE313 4.9 69.2 1.0 C9 A:LFZ501 4.9 84.4 1.0 CZ A:PHE346 4.9 73.7 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:83.4 occ:1.00 F2 A:LFZ501 0.0 83.4 1.0 C11 A:LFZ501 1.3 84.8 1.0 F A:LFZ501 2.1 92.0 1.0 F1 A:LFZ501 2.1 92.5 1.0 C10 A:LFZ501 2.3 85.0 1.0 C12 A:LFZ501 2.8 78.1 1.0 CB A:HIS435 3.4 64.0 1.0 CA A:CYS432 3.5 59.2 1.0 C9 A:LFZ501 3.5 84.4 1.0 O A:CYS432 3.6 58.4 1.0 SG A:CYS432 3.7 64.9 1.0 CB A:CYS432 3.8 63.9 1.0 CG A:HIS435 3.8 65.3 1.0 ND1 A:HIS435 4.0 70.7 1.0 C A:CYS432 4.0 60.8 1.0 C13 A:LFZ501 4.2 78.7 1.0 CE2 A:PHE439 4.5 65.5 1.0 CG2 A:ILE345 4.5 61.2 1.0 N A:CYS432 4.7 55.5 1.0 C8 A:LFZ501 4.7 82.9 1.0 CG A:LEU436 4.7 67.1 1.0 CA A:HIS435 4.8 63.8 1.0 CZ A:PHE439 4.8 66.2 1.0 CD2 A:HIS435 4.8 70.1 1.0 CD2 A:LEU436 4.9 71.1 1.0 CG1 A:ILE345 4.9 58.0 1.0 CE1 A:HIS435 4.9 70.7 1.0 C15 A:LFZ501 5.0 80.8 1.0 O A:LYS431 5.0 54.2 1.0 N A:LEU436 5.0 62.4 1.0 F5 A:LFZ501 5.0 84.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:92.5 occ:1.00 F1 A:LFZ501 0.0 92.5 1.0 C11 A:LFZ501 1.3 84.8 1.0 F2 A:LFZ501 2.1 83.4 1.0 F A:LFZ501 2.1 92.0 1.0 C10 A:LFZ501 2.4 85.0 1.0 C9 A:LFZ501 2.7 84.4 1.0 CD2 A:LEU436 3.0 71.1 1.0 CG A:LEU436 3.1 67.1 1.0 O A:CYS432 3.6 58.4 1.0 CD1 A:LEU436 3.6 66.6 1.0 C12 A:LFZ501 3.6 78.1 1.0 CB A:CYS432 4.1 63.9 1.0 C8 A:LFZ501 4.1 82.9 1.0 CE2 A:PHE439 4.1 65.5 1.0 C A:CYS432 4.2 60.8 1.0 CA A:CYS432 4.2 59.2 1.0 CB A:HIS435 4.4 64.0 1.0 CB A:LEU436 4.5 65.1 1.0 SG A:CYS432 4.5 64.9 1.0 CG2 A:ILE268 4.6 74.8 1.0 N A:LEU436 4.6 62.4 1.0 C13 A:LFZ501 4.7 78.7 1.0 CA A:LEU436 4.8 63.4 1.0 CD2 A:PHE439 4.9 66.2 1.0 C15 A:LFZ501 5.0 80.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175)


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 the Retinoic Acid Receptor Alpha in Complex with Compound 24 (JP175) within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:92.0 occ:1.00 F A:LFZ501 0.0 92.0 1.0 C11 A:LFZ501 1.3 84.8 1.0 F2 A:LFZ501 2.1 83.4 1.0 F1 A:LFZ501 2.1 92.5 1.0 C10 A:LFZ501 2.3 85.0 1.0 C12 A:LFZ501 3.0 78.1 1.0 CE2 A:PHE439 3.2 65.5 1.0 C9 A:LFZ501 3.3 84.4 1.0 CZ A:PHE439 3.7 66.2 1.0 CG2 A:ILE268 4.1 74.8 1.0 CB A:HIS435 4.2 64.0 1.0 CD2 A:LEU436 4.2 71.1 1.0 C13 A:LFZ501 4.2 78.7 1.0 CD2 A:PHE439 4.4 66.2 1.0 C8 A:LFZ501 4.5 82.9 1.0 CG A:LEU436 4.7 67.1 1.0 CG A:HIS435 4.7 65.3 1.0 C15 A:LFZ501 4.8 80.8 1.0 CG1 A:VAL342 4.9 59.2 1.0 O A:CYS432 4.9 58.4 1.0 CD1 A:ILE268 4.9 77.0 1.0

J.Pollinger, S.Schierle, L.Gellrich, J.Ohrndorf, A.Kaiser, P.Heitel, A.Chaikuad, S.Knapp, D.Merk. A Novel Biphenyl-Based Chemotype of Retinoid X Receptor Ligands Enables Subtype and Heterodimer Preferences. Acs Med.Chem.Lett. V. 10 1346 2019.
ISSN: ISSN 1948-5875
PubMed: 31531208
DOI: 10.1021/ACSMEDCHEMLETT.9B00306