Fluorine in PDB 8eqz: Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6

The structure of Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6, PDB code: 8eqz was solved by A.D.Huber, S.Poudel, J.Seetharaman, D.J.Miller, W.Lin, Y.Li, T.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.57 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.371, 89.004, 105.565, 90, 90, 90
R / Rfree (%)	20.4 / 22.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 (pdb code 8eqz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6, PDB code: 8eqz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:83.6 occ:1.00 F35 A:WQB501 0.0 83.6 1.0 C34 A:WQB501 1.4 79.6 1.0 F37 A:WQB501 2.2 86.8 1.0 F36 A:WQB501 2.2 84.1 1.0 F41 A:WQB501 2.4 77.1 1.0 C33 A:WQB501 2.4 85.0 1.0 C38 A:WQB501 2.8 90.1 1.0 C27 A:WQB501 3.1 90.3 1.0 C26 A:WQB501 3.1 98.2 1.0 CB A:MET243 3.3 47.8 1.0 O42 A:WQB501 3.5 76.0 1.0 F40 A:WQB501 3.5 86.3 1.0 CD2 A:LEU240 3.7 59.7 1.0 CE2 A:PHE420 3.9 49.6 1.0 F39 A:WQB501 3.9 86.9 1.0 CG A:MET243 4.0 60.5 1.0 C28 A:WQB501 4.4 95.2 1.0 C A:MET243 4.4 43.5 1.0 C25 A:WQB501 4.5 93.9 1.0 CZ A:PHE420 4.5 52.8 1.0 CA A:MET243 4.5 42.7 1.0 N A:ALA244 4.6 40.6 1.0 O A:LEU240 4.7 45.2 1.0 O A:MET243 4.8 41.8 1.0 CA A:LEU240 4.8 51.2 1.0 CD2 A:PHE420 4.9 49.0 1.0 CD2 A:LEU209 4.9 106.8 1.0

Fluorine binding site 2 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:84.1 occ:1.00 F36 A:WQB501 0.0 84.1 1.0 C34 A:WQB501 1.4 79.6 1.0 F37 A:WQB501 2.1 86.8 1.0 F35 A:WQB501 2.2 83.6 1.0 C33 A:WQB501 2.4 85.0 1.0 O42 A:WQB501 2.9 76.0 1.0 C26 A:WQB501 2.9 98.2 1.0 OG A:SER247 3.0 66.3 1.0 O A:MET243 3.4 41.8 1.0 C27 A:WQB501 3.5 90.3 1.0 CB A:MET243 3.5 47.8 1.0 C A:MET243 3.6 43.5 1.0 C25 A:WQB501 3.7 93.9 1.0 C38 A:WQB501 3.7 90.1 1.0 N A:ALA244 4.0 40.6 1.0 CB A:SER247 4.0 37.9 1.0 F41 A:WQB501 4.1 77.1 1.0 CA A:MET243 4.2 42.7 1.0 CA A:ALA244 4.3 43.3 1.0 F40 A:WQB501 4.4 86.3 1.0 CG A:MET243 4.5 60.5 1.0 C28 A:WQB501 4.6 95.2 1.0 C24 A:WQB501 4.7 100.8 1.0 CE2 A:PHE420 4.8 49.6 1.0 F39 A:WQB501 4.8 86.9 1.0 CE A:MET425 4.8 48.6 1.0

Fluorine binding site 3 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:86.8 occ:1.00 F37 A:WQB501 0.0 86.8 1.0 C34 A:WQB501 1.4 79.6 1.0 F36 A:WQB501 2.1 84.1 1.0 F35 A:WQB501 2.2 83.6 1.0 C33 A:WQB501 2.5 85.0 1.0 O42 A:WQB501 2.7 76.0 1.0 CE2 A:PHE420 2.9 49.6 1.0 C38 A:WQB501 3.1 90.1 1.0 F40 A:WQB501 3.1 86.3 1.0 CZ A:PHE420 3.4 52.8 1.0 F41 A:WQB501 3.4 77.1 1.0 CE A:MET425 3.6 48.6 1.0 C26 A:WQB501 3.8 98.2 1.0 CD1 A:LEU411 3.9 65.5 1.0 CD2 A:PHE420 4.1 49.0 1.0 F39 A:WQB501 4.4 86.9 1.0 C27 A:WQB501 4.5 90.3 1.0 CA A:ALA244 4.6 43.3 1.0 N A:ALA244 4.6 40.6 1.0 OG A:SER247 4.6 66.3 1.0 CB A:MET243 4.7 47.8 1.0 CE1 A:PHE420 4.7 44.4 1.0 SD A:MET425 4.8 48.8 1.0 C A:MET243 4.8 43.5 1.0 CB A:ALA244 4.8 44.8 1.0 C25 A:WQB501 4.8 93.9 1.0 O A:MET243 4.9 41.8 1.0 CD2 A:LEU240 5.0 59.7 1.0

Fluorine binding site 4 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:86.9 occ:1.00 F39 A:WQB501 0.0 86.9 1.0 C38 A:WQB501 1.4 90.1 1.0 F41 A:WQB501 2.1 77.1 1.0 F40 A:WQB501 2.1 86.3 1.0 C33 A:WQB501 2.5 85.0 1.0 C26 A:WQB501 2.8 98.2 1.0 C1 A:WQB501 3.0 79.2 1.0 C27 A:WQB501 3.2 90.3 1.0 O42 A:WQB501 3.2 76.0 1.0 C2 A:WQB501 3.5 94.4 1.0 CD2 A:HIS407 3.5 55.9 1.0 NE2 A:HIS407 3.7 67.3 1.0 C34 A:WQB501 3.7 79.6 1.0 C25 A:WQB501 3.7 93.9 1.0 F35 A:WQB501 3.9 83.6 1.0 C28 A:WQB501 4.3 95.2 1.0 F37 A:WQB501 4.4 86.8 1.0 C3 A:WQB501 4.6 103.6 1.0 C24 A:WQB501 4.7 100.8 1.0 CD1 A:ILE414 4.7 56.3 1.0 CG A:HIS407 4.8 65.0 1.0 F36 A:WQB501 4.8 84.1 1.0 C23 A:WQB501 5.0 106.3 1.0 CE1 A:HIS407 5.0 61.0 1.0

Fluorine binding site 5 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:86.3 occ:1.00 F40 A:WQB501 0.0 86.3 1.0 C38 A:WQB501 1.4 90.1 1.0 F41 A:WQB501 2.1 77.1 1.0 F39 A:WQB501 2.1 86.9 1.0 C33 A:WQB501 2.5 85.0 1.0 O42 A:WQB501 2.8 76.0 1.0 F37 A:WQB501 3.1 86.8 1.0 C34 A:WQB501 3.1 79.6 1.0 CD1 A:LEU411 3.4 65.5 1.0 F35 A:WQB501 3.5 83.6 1.0 CZ A:PHE420 3.7 52.8 1.0 CB A:LEU411 3.8 46.9 1.0 C26 A:WQB501 3.8 98.2 1.0 NE2 A:HIS407 3.8 67.3 1.0 CG A:LEU411 4.0 61.3 1.0 CA A:LEU411 4.0 53.5 1.0 CD1 A:ILE414 4.1 56.3 1.0 CD2 A:HIS407 4.2 55.9 1.0 CE2 A:PHE420 4.3 49.6 1.0 F36 A:WQB501 4.4 84.1 1.0 C27 A:WQB501 4.4 90.3 1.0 N A:LEU411 4.6 48.6 1.0 CE1 A:PHE420 4.7 44.4 1.0 CE1 A:HIS407 4.8 61.0 1.0 C25 A:WQB501 4.8 93.9 1.0

Fluorine binding site 6 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:77.1 occ:1.00 F41 A:WQB501 0.0 77.1 1.0 C38 A:WQB501 1.4 90.1 1.0 F39 A:WQB501 2.1 86.9 1.0 F40 A:WQB501 2.1 86.3 1.0 F35 A:WQB501 2.4 83.6 1.0 C33 A:WQB501 2.5 85.0 1.0 C34 A:WQB501 2.8 79.6 1.0 C27 A:WQB501 3.2 90.3 1.0 C26 A:WQB501 3.3 98.2 1.0 F37 A:WQB501 3.4 86.8 1.0 O42 A:WQB501 3.6 76.0 1.0 CD2 A:LEU240 3.7 59.7 1.0 F36 A:WQB501 4.1 84.1 1.0 C1 A:WQB501 4.3 79.2 1.0 CZ A:PHE420 4.4 52.8 1.0 CD1 A:ILE414 4.4 56.3 1.0 CD2 A:LEU206 4.5 82.3 1.0 C28 A:WQB501 4.5 95.2 1.0 CE2 A:PHE420 4.6 49.6 1.0 C25 A:WQB501 4.6 93.9 1.0 CD2 A:LEU209 4.8 106.8 1.0

Fluorine binding site 7 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:89.0 occ:1.00 F35 B:WQB501 0.0 89.0 1.0 C34 B:WQB501 1.4 97.0 1.0 F36 B:WQB501 2.1 82.2 1.0 F37 B:WQB501 2.2 102.7 1.0 C33 B:WQB501 2.4 103.8 1.0 C26 B:WQB501 2.8 101.2 1.0 O42 B:WQB501 2.9 86.6 1.0 OG B:SER247 3.1 64.5 1.0 C27 B:WQB501 3.3 104.1 1.0 O B:MET243 3.5 55.2 1.0 CG B:MET243 3.7 80.7 1.0 C38 B:WQB501 3.7 103.5 1.0 C25 B:WQB501 3.7 89.0 1.0 CB B:MET243 3.8 54.8 1.0 C B:MET243 3.9 52.4 1.0 CB B:SER247 3.9 49.9 1.0 F39 B:WQB501 4.0 103.9 1.0 F41 B:WQB501 4.3 100.8 1.0 C28 B:WQB501 4.4 108.5 1.0 CA B:MET243 4.4 51.8 1.0 N B:ALA244 4.4 53.8 1.0 C24 B:WQB501 4.7 96.3 1.0 CA B:ALA244 4.8 55.3 1.0 F40 B:WQB501 4.8 95.2 1.0

Fluorine binding site 8 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


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 Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:82.2 occ:1.00 F36 B:WQB501 0.0 82.2 1.0 C34 B:WQB501 1.4 97.0 1.0 F37 B:WQB501 2.1 102.7 1.0 F35 B:WQB501 2.1 89.0 1.0 C33 B:WQB501 2.5 103.8 1.0 O42 B:WQB501 2.7 86.6 1.0 F41 B:WQB501 2.9 100.8 1.0 C38 B:WQB501 3.1 103.5 1.0 CE2 B:PHE420 3.2 65.2 1.0 F39 B:WQB501 3.6 103.9 1.0 C26 B:WQB501 3.8 101.2 1.0 CZ B:PHE420 3.8 69.5 1.0 CD1 B:LEU411 4.1 74.4 1.0 CE B:MET425 4.1 49.6 1.0 CD2 B:PHE420 4.2 67.3 1.0 F40 B:WQB501 4.4 95.2 1.0 C27 B:WQB501 4.4 104.1 1.0 CB B:MET243 4.5 54.8 1.0 CD2 B:LEU240 4.5 59.6 1.0 N B:ALA244 4.7 53.8 1.0 C B:MET243 4.7 52.4 1.0 O B:MET243 4.7 55.2 1.0 CA B:ALA244 4.7 55.3 1.0 OG B:SER247 4.8 64.5 1.0 C25 B:WQB501 4.9 89.0 1.0 CG B:MET243 4.9 80.7 1.0

Fluorine binding site 9 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:102.7 occ:1.00 F37 B:WQB501 0.0 102.7 1.0 C34 B:WQB501 1.4 97.0 1.0 F36 B:WQB501 2.1 82.2 1.0 F35 B:WQB501 2.2 89.0 1.0 C33 B:WQB501 2.5 103.8 1.0 F39 B:WQB501 2.5 103.9 1.0 C38 B:WQB501 2.7 103.5 1.0 C27 B:WQB501 3.1 104.1 1.0 C26 B:WQB501 3.2 101.2 1.0 F41 B:WQB501 3.2 100.8 1.0 CG B:MET243 3.2 80.7 1.0 CB B:MET243 3.2 54.8 1.0 O42 B:WQB501 3.5 86.6 1.0 CD2 B:LEU240 3.8 59.6 1.0 F40 B:WQB501 4.1 95.2 1.0 C28 B:WQB501 4.4 108.5 1.0 CE2 B:PHE420 4.4 65.2 1.0 CA B:MET243 4.5 51.8 1.0 C B:MET243 4.5 52.4 1.0 C25 B:WQB501 4.6 89.0 1.0 O B:MET243 4.7 55.2 1.0 N B:ALA244 4.9 53.8 1.0

Fluorine binding site 10 out of 12 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-C6 within 5.0Å range: probe atom residue distance (Å) B Occ B:F501 b:103.9 occ:1.00 F39 B:WQB501 0.0 103.9 1.0 C38 B:WQB501 1.4 103.5 1.0 F40 B:WQB501 2.1 95.2 1.0 F41 B:WQB501 2.1 100.8 1.0 C33 B:WQB501 2.4 103.8 1.0 F37 B:WQB501 2.5 102.7 1.0 C34 B:WQB501 2.9 97.0 1.0 C27 B:WQB501 2.9 104.1 1.0 C26 B:WQB501 3.0 101.2 1.0 O42 B:WQB501 3.6 86.6 1.0 F36 B:WQB501 3.6 82.2 1.0 F35 B:WQB501 4.0 89.0 1.0 C28 B:WQB501 4.1 108.5 1.0 C25 B:WQB501 4.3 89.0 1.0 CD2 B:LEU240 4.4 59.6 1.0 CD1 B:LEU209 4.6 95.3 1.0 CD2 B:LEU206 4.7 87.3 1.0 C1 B:WQB501 4.8 92.0 1.0 CD1 B:ILE414 5.0 64.9 1.0

W.Lin, A.D.Huber, S.Poudel, Y.Li, J.Seetharaman, D.J.Miller, T.Chen. Structure-Guided Approach to Modulate Small Molecule Binding to A Promiscuous Ligand-Activated Protein. Proc.Natl.Acad.Sci.Usa V. 120 04120 2023.
ISSN: ESSN 1091-6490
PubMed: 36848571
DOI: 10.1073/PNAS.2217804120