Fluorine in PDB 8pp0: Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147

The structure of Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147, PDB code: 8pp0 was solved by A.Chaikuad, J.Pollinger, 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)	42.85 / 1.90
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	65.648, 65.648, 110.816, 90, 90, 90
R / Rfree (%)	18 / 22.3

The binding sites of Fluorine atom in the Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147 (pdb code 8pp0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147, PDB code: 8pp0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147


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 Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:65.7 occ:1.00 F2 A:7QJ501 0.0 65.7 1.0 C4 A:7QJ501 1.3 70.9 1.0 F A:7QJ501 2.2 75.8 1.0 F1 A:7QJ501 2.2 73.0 1.0 C3 A:7QJ501 2.4 61.2 1.0 C2 A:7QJ501 2.7 59.6 1.0 CB A:CYS432 3.0 41.5 1.0 N1 A:7QJ501 3.5 55.8 1.0 CD1 A:ILE310 3.7 39.2 1.0 SG A:CYS432 3.9 43.6 1.0 CG1 A:ILE310 4.0 36.5 1.0 C1 A:7QJ501 4.1 63.9 1.0 CD1 A:LEU436 4.2 51.9 1.0 CA A:CYS432 4.2 41.6 1.0 C A:CYS432 4.3 42.7 1.0 CB A:ASN306 4.5 45.5 1.0 O A:CYS432 4.5 42.6 1.0 C11 A:7QJ501 4.5 62.4 1.0 C5 A:7QJ501 4.6 52.7 1.0 N A:LEU433 4.7 41.2 1.0 CG A:LEU436 4.8 49.2 1.0 O A:ASN306 4.8 38.5 1.0 C12 A:7QJ501 4.9 57.4 1.0 N2 A:7QJ501 4.9 57.0 1.0 C10 A:7QJ501 4.9 62.2 1.0 CA A:ASN306 4.9 41.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147


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 Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:73.0 occ:1.00 F1 A:7QJ501 0.0 73.0 1.0 C4 A:7QJ501 1.3 70.9 1.0 F A:7QJ501 2.1 75.8 1.0 F2 A:7QJ501 2.2 65.7 1.0 C3 A:7QJ501 2.4 61.2 1.0 N1 A:7QJ501 2.9 55.8 1.0 O A:ASN306 3.1 38.5 1.0 CA A:ASN306 3.4 41.9 1.0 CG1 A:ILE310 3.4 36.5 1.0 C2 A:7QJ501 3.4 59.6 1.0 CB A:ASN306 3.6 45.5 1.0 CD1 A:ILE310 3.6 39.2 1.0 C A:ASN306 3.6 40.5 1.0 CB A:LEU309 4.1 41.0 1.0 C5 A:7QJ501 4.1 52.7 1.0 CZ3 A:TRP305 4.1 42.7 1.0 N A:ILE310 4.4 36.2 1.0 CE3 A:TRP305 4.5 44.0 1.0 C1 A:7QJ501 4.6 63.9 1.0 CD1 A:LEU309 4.6 47.7 1.0 CB A:ILE310 4.7 35.6 1.0 N A:ASN306 4.7 39.3 1.0 CH2 A:TRP305 4.8 42.1 1.0 CG A:LEU309 4.8 44.8 1.0 O A:TRP305 4.8 36.7 1.0 O A:7QJ501 4.8 53.7 1.0 N2 A:7QJ501 4.9 57.0 1.0 CB A:CYS432 4.9 41.5 1.0 N A:GLU307 4.9 39.0 1.0 CE2 A:PHE313 5.0 42.0 1.0 CA A:ILE310 5.0 35.1 1.0 CG A:ASN306 5.0 58.3 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147


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 Retinoic Acid Receptor Alpha (Rxra) in Complexed with JP147 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:75.8 occ:1.00 F A:7QJ501 0.0 75.8 1.0 C4 A:7QJ501 1.3 70.9 1.0 F1 A:7QJ501 2.1 73.0 1.0 F2 A:7QJ501 2.2 65.7 1.0 C3 A:7QJ501 2.3 61.2 1.0 N1 A:7QJ501 2.8 55.8 1.0 CD1 A:LEU436 3.2 51.9 1.0 CZ3 A:TRP305 3.3 42.7 1.0 C2 A:7QJ501 3.4 59.6 1.0 CH2 A:TRP305 3.6 42.1 1.0 C5 A:7QJ501 4.0 52.7 1.0 CG A:LEU436 4.3 49.2 1.0 CE3 A:TRP305 4.3 44.0 1.0 CB A:ASN306 4.4 45.5 1.0 C1 A:7QJ501 4.5 63.9 1.0 CA A:ASN306 4.6 41.9 1.0 CD2 A:LEU436 4.7 53.1 1.0 N2 A:7QJ501 4.8 57.0 1.0 CB A:ALA272 4.8 45.0 1.0 CZ2 A:TRP305 4.9 43.6 1.0 O A:7QJ501 4.9 53.7 1.0 CD1 A:LEU309 5.0 47.7 1.0 CB A:CYS432 5.0 41.5 1.0

M.Lewandowski, M.Carmina, L.Knumann, M.Sai, S.Willems, T.Kasch, J.Pollinger, S.Knapp, J.A.Marschner, A.Chaikuad, D.Merk. Structure-Guided Design of A Highly Potent Partial Rxr Agonist with Superior Physicochemical Properties. J.Med.Chem. 2024.
ISSN: ISSN 0022-2623
PubMed: 38237049
DOI: 10.1021/ACS.JMEDCHEM.3C02095