Fluorine in PDB 5jy3: Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927

The structure of Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927, PDB code: 5jy3 was solved by J.K.Muckelbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.01 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.660, 120.350, 55.720, 90.00, 107.49, 90.00
R / Rfree (%)	22.5 / 26.8

The structure of Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Fluorine atom in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 (pdb code 5jy3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927, PDB code: 5jy3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:51.8 occ:1.00 F1 A:6OX501 0.0 51.8 1.0 C9 A:6OX501 1.3 48.0 1.0 C23 A:6OX501 2.2 50.6 1.0 C8 A:6OX501 2.3 48.2 1.0 C24 A:6OX501 2.6 49.1 1.0 CB A:GLU315 3.0 38.6 1.0 O4 A:6OX501 3.3 55.6 1.0 C22 A:6OX501 3.5 47.6 1.0 O A:MET312 3.5 37.0 1.0 C7 A:6OX501 3.6 50.8 1.0 CG A:GLU315 3.8 44.0 1.0 OG A:SER278 3.8 44.8 1.0 CA A:MET312 3.9 37.8 1.0 OG1 A:THR316 3.9 36.0 1.0 C10 A:6OX501 4.0 48.0 1.0 N A:THR316 4.1 35.7 1.0 C A:GLU315 4.1 36.2 1.0 C A:MET312 4.2 37.7 1.0 CA A:GLU315 4.2 37.8 1.0 CB A:MET312 4.5 37.7 1.0 CG A:MET312 4.6 37.9 1.0 O A:GLU315 4.6 36.5 1.0 CB A:SER278 4.7 43.8 1.0 CD A:ARG319 4.7 46.9 1.0 C12 A:6OX501 4.7 52.7 1.0 CE1 A:PHE329 4.7 45.4 1.0 CA A:THR316 4.8 35.7 1.0 CD A:GLU315 4.8 49.0 1.0 O A:ILE311 4.8 38.3 1.0 OE2 A:GLU315 4.9 51.4 1.0 N A:GLU315 4.9 36.9 1.0 S1 A:6OX501 4.9 45.8 1.0 N A:MET312 5.0 37.1 1.0 CB A:THR316 5.0 35.4 1.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:56.7 occ:1.00 F2 A:6OX501 0.0 56.7 1.0 C27 A:6OX501 1.3 57.2 1.0 C14 A:6OX501 2.4 57.6 1.0 C26 A:6OX501 2.4 56.7 1.0 N2 A:6OX501 2.8 60.0 1.0 CL1 A:6OX501 3.0 76.3 1.0 CD2 A:PHE271 3.3 48.6 1.0 C3 A:6OX501 3.3 75.5 1.0 C17 A:6OX501 3.3 61.1 1.0 C21 A:6OX501 3.6 76.3 1.0 CG A:PHE271 3.6 47.8 1.0 CB A:PHE271 3.6 47.2 1.0 C15 A:6OX501 3.6 54.7 1.0 C12 A:6OX501 3.7 52.7 1.0 C13 A:6OX501 3.8 63.5 1.0 O A:PHE271 4.0 50.5 1.0 CE2 A:PHE271 4.0 44.9 1.0 C4 A:6OX501 4.0 70.9 1.0 CA A:PHE271 4.1 49.0 1.0 CE2 A:PHE329 4.1 50.9 1.0 C11 A:6OX501 4.1 52.6 1.0 CE1 A:PHE340 4.3 60.1 1.0 C16 A:6OX501 4.3 60.6 1.0 C A:PHE271 4.4 49.8 1.0 CB A:LEU274 4.5 43.8 1.0 C1 A:6OX501 4.5 74.2 1.0 CD1 A:PHE271 4.5 47.8 1.0 N1 A:6OX501 4.5 63.3 1.0 CZ A:PHE329 4.6 50.2 1.0 C5 A:6OX501 4.6 66.5 1.0 C7 A:6OX501 4.8 50.8 1.0 CZ A:PHE271 4.9 46.2 1.0 C6 A:6OX501 4.9 73.9 1.0 CD2 A:PHE329 4.9 48.5 1.0 CD1 A:PHE340 4.9 60.9 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:42.7 occ:1.00 F1 B:6OX501 0.0 42.7 1.0 C9 B:6OX501 1.3 44.7 1.0 C23 B:6OX501 2.4 45.0 1.0 C8 B:6OX501 2.4 42.9 1.0 C24 B:6OX501 2.8 46.0 1.0 O4 B:6OX501 3.0 49.7 1.0 CB B:GLU315 3.1 37.1 1.0 OG B:SER278 3.3 47.9 1.0 C22 B:6OX501 3.6 45.1 1.0 C7 B:6OX501 3.6 43.3 1.0 CA B:MET312 3.7 33.6 1.0 O B:MET312 3.7 36.9 1.0 CG B:GLU315 3.9 39.5 1.0 C10 B:6OX501 4.1 40.9 1.0 CG B:MET312 4.1 32.3 1.0 C B:MET312 4.2 34.5 1.0 CB B:MET312 4.3 33.9 1.0 CA B:GLU315 4.3 36.8 1.0 N B:THR316 4.3 37.3 1.0 C B:GLU315 4.4 37.6 1.0 CB B:SER278 4.4 45.5 1.0 OG1 B:THR316 4.4 37.6 1.0 N B:MET312 4.6 33.5 1.0 O B:ILE311 4.7 33.4 1.0 OE2 B:GLU315 4.8 40.1 1.0 C12 B:6OX501 4.8 42.6 1.0 N B:GLU315 4.8 35.4 1.0 CE1 B:PHE329 4.9 39.9 1.0 CD B:GLU315 4.9 37.2 1.0 O B:GLU315 5.0 38.7 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:51.8 occ:1.00 F2 B:6OX501 0.0 51.8 1.0 C27 B:6OX501 1.3 44.7 1.0 C26 B:6OX501 2.3 43.4 1.0 C14 B:6OX501 2.4 46.7 1.0 N2 B:6OX501 3.0 47.4 1.0 CD1 B:PHE271 3.2 47.5 1.0 CL1 B:6OX501 3.3 68.3 1.0 CB B:PHE271 3.3 47.5 1.0 C17 B:6OX501 3.5 48.5 1.0 CG B:PHE271 3.5 44.7 1.0 O B:PHE271 3.5 46.7 1.0 C12 B:6OX501 3.6 42.6 1.0 C3 B:6OX501 3.6 65.2 1.0 C15 B:6OX501 3.6 45.2 1.0 CA B:PHE271 3.8 46.9 1.0 C13 B:6OX501 3.9 51.1 1.0 C21 B:6OX501 4.0 62.3 1.0 C B:PHE271 4.0 47.0 1.0 C11 B:6OX501 4.0 42.9 1.0 CE2 B:PHE329 4.2 39.9 1.0 CE1 B:PHE271 4.2 49.9 1.0 CE1 B:PHE340 4.2 43.7 1.0 C4 B:6OX501 4.3 59.4 1.0 CB B:LEU274 4.4 46.0 1.0 C16 B:6OX501 4.5 50.3 1.0 CD2 B:LEU274 4.5 42.1 1.0 CD2 B:PHE271 4.7 45.1 1.0 CD2 B:PHE329 4.7 41.9 1.0 C5 B:6OX501 4.7 54.5 1.0 C7 B:6OX501 4.7 43.3 1.0 N1 B:6OX501 4.7 50.6 1.0 CZ B:PHE329 4.8 40.0 1.0 C1 B:6OX501 4.9 63.9 1.0 CD1 B:PHE340 5.0 46.0 1.0 N B:ALA275 5.0 46.0 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:49.4 occ:1.00 F1 C:6OX501 0.0 49.4 1.0 C9 C:6OX501 1.3 50.8 1.0 C23 C:6OX501 2.3 52.4 1.0 C8 C:6OX501 2.3 52.0 1.0 O4 C:6OX501 2.6 59.3 1.0 C24 C:6OX501 2.8 51.5 1.0 CB C:GLU315 3.2 40.8 1.0 O C:MET312 3.4 40.6 1.0 OG C:SER278 3.5 39.6 1.0 C22 C:6OX501 3.6 51.1 1.0 C7 C:6OX501 3.6 54.2 1.0 CA C:MET312 3.6 39.2 1.0 CG C:GLU315 3.9 46.1 1.0 C C:MET312 4.0 39.2 1.0 C10 C:6OX501 4.1 50.9 1.0 N C:THR316 4.2 41.4 1.0 OG1 C:THR316 4.3 37.8 1.0 CB C:MET312 4.3 39.0 1.0 CG C:MET312 4.3 36.1 1.0 CA C:GLU315 4.4 41.0 1.0 C C:GLU315 4.4 40.6 1.0 CB C:SER278 4.5 42.1 1.0 O C:ILE311 4.6 40.4 1.0 N C:MET312 4.7 38.0 1.0 C12 C:6OX501 4.7 53.5 1.0 OE2 C:GLU315 4.8 52.7 1.0 CE1 C:PHE329 4.8 50.3 1.0 CD C:GLU315 4.9 52.0 1.0 N C:GLU315 5.0 40.1 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


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 Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ C:F501 b:57.6 occ:1.00 F2 C:6OX501 0.0 57.6 1.0 C27 C:6OX501 1.3 58.8 1.0 C14 C:6OX501 2.3 59.1 1.0 C26 C:6OX501 2.4 57.5 1.0 N2 C:6OX501 2.6 60.9 1.0 C29 C:6OX501 2.9 59.5 1.0 C13 C:6OX501 3.1 62.3 1.0 CD2 C:PHE271 3.2 50.3 1.0 C17 C:6OX501 3.3 60.3 1.0 CB C:PHE271 3.5 48.4 1.0 CG C:PHE271 3.5 47.9 1.0 C5 C:6OX501 3.6 65.6 1.0 C15 C:6OX501 3.6 53.9 1.0 C12 C:6OX501 3.6 53.5 1.0 O C:PHE271 3.7 51.5 1.0 N1 C:6OX501 3.9 60.9 1.0 CA C:PHE271 4.0 49.1 1.0 C16 C:6OX501 4.0 58.2 1.0 CE2 C:PHE271 4.1 50.3 1.0 C11 C:6OX501 4.1 53.6 1.0 C C:PHE271 4.2 50.7 1.0 CL1 C:6OX501 4.2 73.0 1.0 C4 C:6OX501 4.3 67.2 1.0 CE1 C:PHE340 4.3 61.3 1.0 CE2 C:PHE329 4.4 53.3 1.0 C3 C:6OX501 4.5 69.1 1.0 CB C:LEU274 4.6 40.0 1.0 CD1 C:PHE271 4.7 47.5 1.0 CD1 C:PHE340 4.8 62.2 1.0 CZ C:PHE329 4.8 51.4 1.0 C7 C:6OX501 4.8 54.2 1.0 C28 C:6OX501 5.0 65.1 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:46.1 occ:1.00 F1 D:6OX501 0.0 46.1 1.0 C9 D:6OX501 1.3 47.5 1.0 C8 D:6OX501 2.3 46.3 1.0 C23 D:6OX501 2.3 49.1 1.0 C24 D:6OX501 2.8 49.5 1.0 CB D:GLU315 3.1 38.1 1.0 O4 D:6OX501 3.1 47.3 1.0 CG D:GLU315 3.1 40.3 1.0 O D:MET312 3.5 30.7 1.0 C7 D:6OX501 3.6 47.9 1.0 C22 D:6OX501 3.6 48.2 1.0 OG D:SER278 3.7 47.5 1.0 CA D:MET312 3.8 29.8 1.0 C10 D:6OX501 4.1 48.4 1.0 C D:MET312 4.1 30.0 1.0 N D:THR316 4.3 39.6 1.0 CA D:GLU315 4.3 37.6 1.0 CG D:MET312 4.3 32.4 1.0 C D:GLU315 4.4 38.8 1.0 OG1 D:THR316 4.5 41.4 1.0 CB D:MET312 4.5 30.5 1.0 CB D:SER278 4.5 46.5 1.0 CD D:GLU315 4.6 40.5 1.0 C12 D:6OX501 4.8 46.0 1.0 O D:ILE311 4.8 30.7 1.0 N D:MET312 4.8 29.9 1.0 CE1 D:PHE329 4.9 45.3 1.0 N D:GLU315 4.9 36.8 1.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Lxrbeta (Nuclear Receptor Subfamily 1, Group H, Member 2) Complexed with Bms-852927 within 5.0Å range: probe atom residue distance (Å) B Occ D:F501 b:49.3 occ:1.00 F2 D:6OX501 0.0 49.3 1.0 C27 D:6OX501 1.3 48.2 1.0 C26 D:6OX501 2.3 46.8 1.0 C14 D:6OX501 2.4 48.3 1.0 N2 D:6OX501 2.9 49.8 1.0 CD1 D:PHE271 3.2 48.7 1.0 C17 D:6OX501 3.4 49.1 1.0 CB D:PHE271 3.5 48.5 1.0 O D:PHE271 3.5 49.1 1.0 CL1 D:6OX501 3.5 64.4 1.0 C12 D:6OX501 3.6 46.0 1.0 C15 D:6OX501 3.6 45.5 1.0 CG D:PHE271 3.6 49.2 1.0 C3 D:6OX501 3.8 60.4 1.0 CA D:PHE271 3.8 48.9 1.0 C13 D:6OX501 3.9 49.7 1.0 C11 D:6OX501 4.0 45.3 1.0 C D:PHE271 4.0 48.9 1.0 CE1 D:PHE271 4.1 49.5 1.0 CE2 D:PHE329 4.2 44.7 1.0 C21 D:6OX501 4.2 57.7 1.0 CB D:LEU274 4.3 40.6 1.0 C4 D:6OX501 4.3 56.3 1.0 CE1 D:PHE340 4.4 53.5 1.0 C16 D:6OX501 4.4 49.5 1.0 CD2 D:LEU274 4.5 35.1 1.0 C5 D:6OX501 4.7 54.1 1.0 N1 D:6OX501 4.7 50.5 1.0 CZ D:PHE329 4.7 45.3 1.0 C7 D:6OX501 4.7 47.9 1.0 CD2 D:PHE329 4.8 44.8 1.0 CD2 D:PHE271 4.8 47.6 1.0 CG D:LEU274 5.0 40.2 1.0 N D:ALA275 5.0 44.1 1.0

E.K.Kick, B.B.Busch, R.Martin, W.C.Stevens, V.Bollu, Y.Xie, B.C.Boren, M.C.Nyman, M.H.Nanao, L.Nguyen, A.Plonowski, I.G.Schulman, G.Yan, H.Zhang, X.Hou, M.N.Valente, R.Narayanan, K.Behnia, A.D.Rodrigues, B.Brock, J.Smalley, G.H.Cantor, J.Lupisella, P.Sleph, D.Grimm, J.Ostrowski, R.R.Wexler, T.Kirchgessner, R.Mohan. Discovery of Highly Potent Liver X Receptor Beta Agonists. Acs Med Chem Lett V. 7 1207 2016.
ISSN: ISSN 1948-5875
PubMed: 27994765
DOI: 10.1021/ACSMEDCHEMLETT.6B00234