Fluorine in PDB 6br3: Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828.

The structure of Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828., PDB code: 6br3 was solved by R.J.Skene, I.Hoffman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.00
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	99.537, 99.537, 127.524, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.9

The binding sites of Fluorine atom in the Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828. (pdb code 6br3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828., PDB code: 6br3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828. within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:47.0 occ:1.00 F39 A:E3V502 0.0 47.0 1.0 C38 A:E3V502 1.3 48.6 1.0 C40 A:E3V502 2.3 49.8 1.0 C37 A:E3V502 2.4 49.0 1.0 C34 A:E3V502 3.1 48.1 1.0 CD1 A:LEU324 3.2 61.6 1.0 C35 A:E3V502 3.2 45.9 1.0 C36 A:E3V502 3.4 46.9 1.0 CB A:CYS320 3.4 54.9 1.0 CG A:LEU324 3.5 60.9 1.0 SG A:CYS320 3.5 56.4 1.0 C31 A:E3V502 3.6 49.1 1.0 C29 A:E3V502 3.6 51.4 1.0 CA A:CYS320 3.8 55.0 1.0 CD2 A:LEU324 4.0 59.7 1.0 O A:CYS320 4.1 55.8 1.0 C30 A:E3V502 4.1 50.7 1.0 C A:CYS320 4.3 54.9 1.0 C33 A:E3V502 4.4 47.2 1.0 O27 A:E3V502 4.6 50.2 1.0 C32 A:E3V502 4.7 47.5 1.0 N28 A:E3V502 4.8 51.2 1.0 CE1 A:PHE388 4.8 52.4 1.0 CB A:LEU324 4.9 59.7 1.0 CE1 A:PHE378 4.9 50.1 1.0

Fluorine binding site 2 out of 2 in the Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Rorgt in Complex with A Novel Inverse Agonist Tak-828. within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:49.6 occ:1.00 F39 B:E3V502 0.0 49.6 1.0 C38 B:E3V502 1.3 51.5 1.0 C40 B:E3V502 2.3 52.9 1.0 C37 B:E3V502 2.4 51.5 1.0 C34 B:E3V502 3.1 51.7 1.0 CD1 B:LEU324 3.1 56.3 1.0 C35 B:E3V502 3.2 51.5 1.0 CB B:CYS320 3.4 57.1 1.0 CG B:LEU324 3.4 56.3 1.0 C36 B:E3V502 3.4 49.3 1.0 SG B:CYS320 3.5 58.1 1.0 C31 B:E3V502 3.6 52.1 1.0 C29 B:E3V502 3.6 53.9 1.0 CA B:CYS320 3.8 57.2 1.0 CD2 B:LEU324 3.9 53.6 1.0 O B:CYS320 4.0 57.1 1.0 C30 B:E3V502 4.1 53.9 1.0 C B:CYS320 4.2 57.5 1.0 C33 B:E3V502 4.4 51.8 1.0 O27 B:E3V502 4.6 51.3 1.0 C32 B:E3V502 4.7 51.9 1.0 N28 B:E3V502 4.8 53.6 1.0 CB B:LEU324 4.8 56.7 1.0 CE2 B:PHE388 4.8 52.6 1.0 CE1 B:PHE378 4.9 57.1 1.0

M.Kono, A.Ochida, T.Oda, T.Imada, Y.Banno, N.Taya, S.Masada, T.Kawamoto, K.Yonemori, Y.Nara, Y.Fukase, T.Yukawa, H.Tokuhara, R.Skene, B.C.Sang, I.D.Hoffman, G.P.Snell, K.Uga, A.Shibata, K.Igaki, Y.Nakamura, H.Nakagawa, N.Tsuchimori, M.Yamasaki, J.Shirai, S.Yamamoto. Discovery of [ Cis-3-({(5 R)-5-[(7-Fluoro-1,1-Dimethyl-2,3-Dihydro-1 H-Inden-5-Yl)Carbamoyl]-2-Methoxy-7,8-Dihydro-1, 6-Naphthyridin-6(5 H)-Yl}Carbonyl)Cyclobutyl]Acetic Acid (Tak-828F) As A Potent, Selective, and Orally Available Novel Retinoic Acid Receptor-Related Orphan Receptor Gamma T Inverse Agonist. J. Med. Chem. V. 61 2973 2018.
ISSN: ISSN 1520-4804
PubMed: 29510038
DOI: 10.1021/ACS.JMEDCHEM.8B00061