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

The structure of Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp, PDB code: 8fpe 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)	35.54 / 2.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.099, 91.099, 85.215, 90, 90, 90
R / Rfree (%)	21.7 / 24

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

Fluorine binding site 1 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:72.3 occ:1.00 F35 A:Y5B501 0.0 72.3 1.0 C34 A:Y5B501 1.3 77.2 1.0 F36 A:Y5B501 2.1 65.4 1.0 F37 A:Y5B501 2.1 75.7 1.0 C33 A:Y5B501 2.4 79.7 1.0 F41 A:Y5B501 2.6 73.9 1.0 O42 A:Y5B501 2.7 65.0 1.0 C38 A:Y5B501 2.9 82.0 1.0 F40 A:Y5B501 3.4 89.6 1.0 CE2 A:PHE420 3.4 56.2 1.0 C26 A:Y5B501 3.7 78.0 1.0 CD2 A:LEU240 3.9 48.5 1.0 CZ A:PHE420 3.9 48.8 1.0 F39 A:Y5B501 4.1 92.3 1.0 C25 A:Y5B501 4.2 77.0 1.0 CB A:MET243 4.4 45.2 1.0 CD2 A:PHE420 4.5 48.7 1.0 CD1 A:LEU411 4.6 51.5 1.0 CE A:MET425 4.7 46.0 1.0 C27 A:Y5B501 4.8 74.5 1.0 N A:ALA244 5.0 47.2 1.0 C A:MET243 5.0 46.7 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:65.4 occ:1.00 F36 A:Y5B501 0.0 65.4 1.0 C34 A:Y5B501 1.3 77.2 1.0 F35 A:Y5B501 2.1 72.3 1.0 F37 A:Y5B501 2.1 75.7 1.0 C33 A:Y5B501 2.4 79.7 1.0 O42 A:Y5B501 2.7 65.0 1.0 C26 A:Y5B501 2.9 78.0 1.0 C25 A:Y5B501 3.1 77.0 1.0 CB A:MET243 3.4 45.2 1.0 OG A:SER247 3.5 62.8 1.0 C38 A:Y5B501 3.7 82.0 1.0 O A:MET243 3.8 44.4 1.0 C27 A:Y5B501 3.9 74.5 1.0 C A:MET243 3.9 46.7 1.0 F41 A:Y5B501 4.1 73.9 1.0 F40 A:Y5B501 4.2 89.6 1.0 C24 A:Y5B501 4.2 78.5 1.0 CA A:MET243 4.2 51.9 1.0 C05 A:Y5B501 4.3 73.8 1.0 CG A:MET243 4.3 55.7 1.0 N A:ALA244 4.4 47.2 1.0 CB A:SER247 4.6 42.8 1.0 F39 A:Y5B501 4.8 92.3 1.0 C06 A:Y5B501 4.8 79.7 1.0 C04 A:Y5B501 4.8 73.6 1.0 C28 A:Y5B501 4.8 80.8 1.0 C23 A:Y5B501 5.0 86.1 1.0 CA A:ALA244 5.0 51.7 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:75.7 occ:1.00 F37 A:Y5B501 0.0 75.7 1.0 C34 A:Y5B501 1.3 77.2 1.0 F35 A:Y5B501 2.1 72.3 1.0 F36 A:Y5B501 2.1 65.4 1.0 C33 A:Y5B501 2.4 79.7 1.0 F40 A:Y5B501 2.7 89.6 1.0 C25 A:Y5B501 2.7 77.0 1.0 C26 A:Y5B501 2.9 78.0 1.0 C38 A:Y5B501 2.9 82.0 1.0 CB A:MET243 3.3 45.2 1.0 CD2 A:LEU209 3.3 80.2 1.0 F41 A:Y5B501 3.4 73.9 1.0 O42 A:Y5B501 3.5 65.0 1.0 CG A:MET243 3.7 55.7 1.0 C24 A:Y5B501 3.9 78.5 1.0 CD2 A:LEU240 4.1 48.5 1.0 F39 A:Y5B501 4.2 92.3 1.0 C27 A:Y5B501 4.3 74.5 1.0 CG A:LEU209 4.5 81.0 1.0 CA A:MET243 4.7 51.9 1.0 CE A:MET243 4.7 71.8 1.0 CD1 A:LEU209 4.9 82.6 1.0 SD A:MET243 4.9 61.9 1.0 C A:MET243 5.0 46.7 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:92.3 occ:1.00 F39 A:Y5B501 0.0 92.3 1.0 C38 A:Y5B501 1.3 82.0 1.0 F41 A:Y5B501 2.1 73.9 1.0 F40 A:Y5B501 2.1 89.6 1.0 C33 A:Y5B501 2.4 79.7 1.0 O42 A:Y5B501 2.9 65.0 1.0 C26 A:Y5B501 3.0 78.0 1.0 NE2 A:HIS407 3.2 50.8 1.0 CD2 A:HIS407 3.2 49.7 1.0 C27 A:Y5B501 3.3 74.5 1.0 C34 A:Y5B501 3.7 77.2 1.0 C25 A:Y5B501 3.9 77.0 1.0 F35 A:Y5B501 4.1 72.3 1.0 F37 A:Y5B501 4.2 75.7 1.0 CD A:ARG410 4.3 76.3 1.0 CE1 A:HIS407 4.4 48.2 1.0 C28 A:Y5B501 4.5 80.8 1.0 CG A:HIS407 4.5 50.3 1.0 CB A:SER208 4.7 86.5 1.0 F36 A:Y5B501 4.8 65.4 1.0 C24 A:Y5B501 4.9 78.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog T0-Bp


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:89.6 occ:1.00 F40 A:Y5B501 0.0 89.6 1.0 C38 A:Y5B501 1.3 82.0 1.0 F41 A:Y5B501 2.1 73.9 1.0 F39 A:Y5B501 2.1 92.3 1.0 C33 A:Y5B501 2.4 79.7 1.0 F37 A:Y5B501 2.7 75.7 1.0 C34 A:Y5B501 2.9 77.2 1.0 C26 A:Y5B501 2.9 78.0 1.0 C25 A:Y5B501 3.2 77.0 1.0 F35 A:Y5B501 3.4 72.3 1.0 O42 A:Y5B501 3.6 65.0 1.0 C27 A:Y5B501 4.0 74.5 1.0 CD2 A:LEU209 4.0 80.2 1.0 CB A:SER208 4.1 86.5 1.0 F36 A:Y5B501 4.2 65.4 1.0 C24 A:Y5B501 4.4 78.5 1.0 CG A:LEU209 4.6 81.0 1.0 O A:SER208 4.6 90.8 1.0 C A:SER208 4.8 92.0 1.0 CD2 A:LEU240 4.9 48.5 1.0 C28 A:Y5B501 5.0 80.8 1.0

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


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-Bp within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:73.9 occ:1.00 F41 A:Y5B501 0.0 73.9 1.0 C38 A:Y5B501 1.3 82.0 1.0 F40 A:Y5B501 2.1 89.6 1.0 F39 A:Y5B501 2.1 92.3 1.0 C33 A:Y5B501 2.4 79.7 1.0 F35 A:Y5B501 2.6 72.3 1.0 O42 A:Y5B501 2.8 65.0 1.0 C34 A:Y5B501 2.9 77.2 1.0 F37 A:Y5B501 3.4 75.7 1.0 C26 A:Y5B501 3.7 78.0 1.0 F36 A:Y5B501 4.1 65.4 1.0 NE2 A:HIS407 4.1 50.8 1.0 CD1 A:ILE414 4.3 51.6 1.0 CD1 A:LEU411 4.3 51.5 1.0 CZ A:PHE420 4.3 48.8 1.0 C25 A:Y5B501 4.5 77.0 1.0 C27 A:Y5B501 4.6 74.5 1.0 CD2 A:LEU240 4.6 48.5 1.0 CE2 A:PHE420 4.7 56.2 1.0 CD2 A:HIS407 4.7 49.7 1.0 CB A:LEU411 4.7 45.1 1.0 CG A:LEU411 4.8 50.6 1.0 CA A:LEU411 4.8 53.0 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