Fluorine in PDB 7trb: Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide

The structure of Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide, PDB code: 7trb was solved by J.A.Khan, M.Ruzanov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.97 / 2.15
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.71, 119.26, 36.71, 90, 90, 90
R / Rfree (%)	21.4 / 25.6

The binding sites of Fluorine atom in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide (pdb code 7trb). 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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide, PDB code: 7trb:
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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:95.6 occ:1.00 F1 A:IUS501 0.0 95.6 1.0 C19 A:IUS501 1.4 95.3 1.0 C18 A:IUS501 2.4 94.0 1.0 C20 A:IUS501 2.4 95.6 1.0 C21 A:IUS501 2.4 95.5 1.0 H22 A:IUS501 2.7 95.6 0.0 H20 A:IUS501 2.7 95.6 0.0 H19 A:IUS501 2.7 95.6 0.0 H24 A:IUS501 2.7 95.6 0.0 N2 A:IUS501 2.9 91.8 1.0 CZ3 A:TRP473 3.2 66.1 1.0 H21 A:IUS501 3.4 95.6 0.0 H23 A:IUS501 3.4 95.6 0.0 CB A:ALA295 3.4 53.2 1.0 O1 A:IUS501 3.6 94.5 1.0 CH2 A:TRP473 3.8 66.6 1.0 CD1 A:LEU469 4.0 60.9 1.0 NE2 A:HIS451 4.0 51.0 1.0 CE1 A:HIS451 4.1 50.9 1.0 C17 A:IUS501 4.2 93.0 1.0 CE3 A:TRP473 4.2 65.0 1.0 CD2 A:LEU455 4.4 70.4 1.0 N3 A:IUS501 4.6 94.1 1.0 CD2 A:LEU469 4.6 63.6 1.0 CE1 A:PHE465 4.7 89.6 1.0 CG A:LEU469 4.8 61.7 1.0 CA A:ALA295 4.9 52.9 1.0 CE A:MET454 4.9 76.2 1.0 H6 A:IUS501 5.0 95.6 0.0

Fluorine binding site 2 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:93.3 occ:1.00 F2 A:IUS501 0.0 93.3 1.0 C35 A:IUS501 1.3 92.8 1.0 F3 A:IUS501 2.1 90.5 1.0 F4 A:IUS501 2.1 92.4 1.0 C29 A:IUS501 2.4 94.9 1.0 O3 A:IUS501 2.5 95.6 1.0 C30 A:IUS501 3.3 95.6 1.0 CD2 A:LEU344 3.4 95.2 1.0 H31 A:IUS501 3.4 95.6 0.0 H34 A:IUS501 3.5 95.6 0.0 CG2 A:ILE339 3.6 66.4 1.0 C31 A:IUS501 3.7 95.6 1.0 H30 A:IUS501 3.9 95.6 0.0 H32 A:IUS501 4.0 95.6 0.0 CD1 A:LEU344 4.1 92.5 1.0 CB A:THR274 4.3 123.8 1.0 C28 A:IUS501 4.4 95.5 1.0 CG A:LEU344 4.4 92.5 1.0 H33 A:IUS501 4.4 95.6 0.0 CA A:THR274 4.4 117.6 1.0 O A:THR274 4.6 120.7 1.0 CB A:ILE339 4.6 65.3 1.0 H29 A:IUS501 4.6 95.6 0.0 CE1 A:PHE340 4.7 79.9 1.0 CD1 A:PHE340 4.8 78.5 1.0 C A:THR274 5.0 121.4 1.0

Fluorine binding site 3 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:90.5 occ:1.00 F3 A:IUS501 0.0 90.5 1.0 C35 A:IUS501 1.3 92.8 1.0 F2 A:IUS501 2.1 93.3 1.0 F4 A:IUS501 2.1 92.4 1.0 C29 A:IUS501 2.4 94.9 1.0 H31 A:IUS501 2.5 95.6 0.0 C30 A:IUS501 2.8 95.6 1.0 H29 A:IUS501 3.1 95.6 0.0 C31 A:IUS501 3.2 95.6 1.0 H32 A:IUS501 3.3 95.6 0.0 C28 A:IUS501 3.3 95.5 1.0 O3 A:IUS501 3.5 95.6 1.0 H30 A:IUS501 3.7 95.6 0.0 CB A:ILE277 3.9 139.9 1.0 H33 A:IUS501 4.2 95.6 0.0 H34 A:IUS501 4.3 95.6 0.0 CE A:MET294 4.5 72.8 1.0 O A:THR274 4.5 120.7 1.0 CA A:THR274 4.6 117.6 1.0 H1 A:IUS501 4.6 95.6 0.0 C1 A:IUS501 4.7 95.5 1.0 CE1 A:PHE340 4.8 79.9 1.0 CD2 A:LEU344 4.8 95.2 1.0 C27 A:IUS501 4.8 91.9 1.0

Fluorine binding site 4 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:92.4 occ:1.00 F4 A:IUS501 0.0 92.4 1.0 C35 A:IUS501 1.3 92.8 1.0 F3 A:IUS501 2.1 90.5 1.0 F2 A:IUS501 2.1 93.3 1.0 C29 A:IUS501 2.4 94.9 1.0 H32 A:IUS501 2.5 95.6 0.0 C31 A:IUS501 2.9 95.6 1.0 O3 A:IUS501 3.1 95.6 1.0 H33 A:IUS501 3.6 95.6 0.0 C30 A:IUS501 3.7 95.6 1.0 CA A:THR274 3.8 117.6 1.0 CB A:THR274 3.9 123.8 1.0 C28 A:IUS501 3.9 95.5 1.0 H34 A:IUS501 3.9 95.6 0.0 H29 A:IUS501 4.0 95.6 0.0 H31 A:IUS501 4.0 95.6 0.0 N A:THR274 4.5 117.8 1.0 H30 A:IUS501 4.5 95.6 0.0 CG2 A:ILE339 4.6 66.4 1.0 O A:ILE273 4.7 121.2 1.0 O A:THR274 4.8 120.7 1.0 C A:THR274 4.8 121.4 1.0 C A:ILE273 4.9 121.4 1.0

Fluorine binding site 5 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:97.3 occ:1.00 F1 B:IUS501 0.0 97.3 1.0 C19 B:IUS501 1.4 96.3 1.0 C18 B:IUS501 2.4 95.7 1.0 C21 B:IUS501 2.4 95.6 1.0 C20 B:IUS501 2.4 95.6 1.0 H19 B:IUS501 2.6 95.6 0.0 H24 B:IUS501 2.6 95.6 0.0 H22 B:IUS501 2.7 95.6 0.0 H20 B:IUS501 2.8 95.6 0.0 N2 B:IUS501 2.8 94.6 1.0 CZ3 B:TRP473 3.1 53.1 1.0 H21 B:IUS501 3.3 95.6 0.0 H23 B:IUS501 3.3 95.6 0.0 NE2 B:HIS451 3.4 53.7 1.0 CE1 B:HIS451 3.5 53.2 1.0 O1 B:IUS501 3.6 96.1 1.0 CH2 B:TRP473 3.7 53.7 1.0 CD2 B:LEU455 3.8 88.2 1.0 CE3 B:TRP473 4.0 51.7 1.0 CB B:ALA295 4.0 53.4 1.0 C17 B:IUS501 4.1 94.7 1.0 CD1 B:LEU469 4.3 50.8 1.0 CE1 B:PHE465 4.3 86.2 1.0 N3 B:IUS501 4.5 95.4 1.0 CD2 B:HIS451 4.7 53.9 1.0 ND1 B:HIS451 4.7 54.3 1.0 H6 B:IUS501 4.8 95.6 0.0 CZ2 B:TRP473 4.9 53.8 1.0

Fluorine binding site 6 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:100.2 occ:1.00 F2 B:IUS501 0.0 100.2 1.0 C35 B:IUS501 1.3 99.3 1.0 F4 B:IUS501 2.1 98.9 1.0 F3 B:IUS501 2.1 100.7 1.0 C29 B:IUS501 2.4 96.5 1.0 O3 B:IUS501 2.6 95.6 1.0 H32 B:IUS501 3.1 95.6 0.0 C31 B:IUS501 3.2 95.6 1.0 H34 B:IUS501 3.6 95.6 0.0 C30 B:IUS501 3.7 95.5 1.0 H33 B:IUS501 3.8 95.6 0.0 H31 B:IUS501 4.0 95.6 0.0 C28 B:IUS501 4.2 95.5 1.0 H29 B:IUS501 4.4 95.6 0.0 CG2 B:ILE339 4.5 53.1 1.0 H30 B:IUS501 4.5 95.6 0.0 CE B:MET294 4.8 69.1 1.0 N B:ILE277 5.0 118.0 1.0

Fluorine binding site 7 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:100.7 occ:1.00 F3 B:IUS501 0.0 100.7 1.0 C35 B:IUS501 1.3 99.3 1.0 F4 B:IUS501 2.1 98.9 1.0 F2 B:IUS501 2.1 100.2 1.0 C29 B:IUS501 2.4 96.5 1.0 H31 B:IUS501 2.6 95.6 0.0 C30 B:IUS501 2.9 95.5 1.0 O3 B:IUS501 2.9 95.6 1.0 H30 B:IUS501 3.6 95.6 0.0 CD2 B:LEU344 3.6 77.8 1.0 C31 B:IUS501 3.7 95.6 1.0 H34 B:IUS501 3.8 95.6 0.0 CG2 B:ILE339 3.8 53.1 1.0 C28 B:IUS501 4.0 95.5 1.0 H32 B:IUS501 4.0 95.6 0.0 H29 B:IUS501 4.0 95.6 0.0 CD1 B:LEU344 4.4 76.8 1.0 CG B:LEU344 4.4 76.7 1.0 H33 B:IUS501 4.5 95.6 0.0

Fluorine binding site 8 out of 8 in the Crystal Structure of Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide


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 Farnesoid X-Activated Receptor Complexed with Compound-32 Aka (1S,3S)-N-({4-[5-(2-Fluoropr Opan-2-Yl)-1,2,4- Oxadiazol-3-Yl]Bicyclo[2.2.2]Octan-1-Yl}M Ethyl)-3-Hydroxy-N-[4'-(2- Hydroxypropan-2-Yl)-[1,1'-Biphen Yl]-3-Yl]-3-(Trifluoromethyl) Cyclobutane-1-Carboxamide within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:98.9 occ:1.00 F4 B:IUS501 0.0 98.9 1.0 C35 B:IUS501 1.3 99.3 1.0 F2 B:IUS501 2.1 100.2 1.0 F3 B:IUS501 2.1 100.7 1.0 C29 B:IUS501 2.4 96.5 1.0 H32 B:IUS501 2.6 95.6 0.0 H29 B:IUS501 2.8 95.6 0.0 C31 B:IUS501 2.8 95.6 1.0 H31 B:IUS501 3.0 95.6 0.0 C30 B:IUS501 3.1 95.5 1.0 C28 B:IUS501 3.2 95.5 1.0 CE B:MET294 3.5 69.1 1.0 O3 B:IUS501 3.6 95.6 1.0 H33 B:IUS501 3.8 95.6 0.0 H30 B:IUS501 4.1 95.6 0.0 H34 B:IUS501 4.3 95.6 0.0 SD B:MET294 4.6 72.6 1.0 C27 B:IUS501 4.7 93.5 1.0 H1 B:IUS501 4.7 95.6 0.0 C1 B:IUS501 4.8 95.5 1.0

S.J.Nara, S.Jogi, S.Cheruku, S.Kandhasamy, F.Jaipuri, P.K.Kathi, S.Reddy, S.Sarodaya, E.M.Cook, T.Wang, D.Sitkoff, K.A.Rossi, M.Ruzanov, S.E.Kiefer, J.A.Khan, M.Gao, S.Reddy, S.Sivaprasad Lvj, R.Sane, K.Mosure, X.Zhuo, G.G.Cao, M.Ziegler, A.Azzara, J.Krupinski, M.G.Soars, B.A.Ellsworth, D.A.Wacker. Discovery of Bms-986339, A Pharmacologically Differentiated Farnesoid X Receptor Agonist For the Treatment of Nonalcoholic Steatohepatitis. J.Med.Chem. V. 65 8948 2022.
ISSN: ISSN 0022-2623
PubMed: 35704802
DOI: 10.1021/ACS.JMEDCHEM.2C00165