Fluorine in PDB 8szv: Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318

The structure of Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318, PDB code: 8szv was solved by A.D.Huber, S.Poudel, D.J.Miller, Y.Li, T.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.74 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.48, 91.48, 85.08, 90, 90, 90
R / Rfree (%)	21.1 / 22.3

The binding sites of Fluorine atom in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318 (pdb code 8szv). 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 Sjpyt-318, PDB code: 8szv:
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 Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:78.5 occ:1.00 F1 A:X1D501 0.0 78.5 1.0 C25 A:X1D501 1.3 72.7 1.0 F2 A:X1D501 2.1 72.2 1.0 F3 A:X1D501 2.2 76.0 1.0 C24 A:X1D501 2.4 79.7 1.0 F5 A:X1D501 2.5 72.8 1.0 C26 A:X1D501 2.8 92.3 1.0 C23 A:X1D501 2.9 71.5 1.0 C27 A:X1D501 3.0 79.8 1.0 F6 A:X1D501 3.3 79.5 1.0 CB A:MET243 3.4 44.0 1.0 O4 A:X1D501 3.6 66.2 1.0 CG A:MET243 3.8 49.6 1.0 CD2 A:LEU240 3.8 49.3 1.0 F4 A:X1D501 4.1 67.7 1.0 C22 A:X1D501 4.1 71.4 1.0 C28 A:X1D501 4.2 81.3 1.0 CE A:MET243 4.7 64.8 1.0 CA A:MET243 4.9 52.3 1.0 CD2 A:LEU209 4.9 102.9 1.0 SD A:MET243 5.0 57.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:72.2 occ:1.00 F2 A:X1D501 0.0 72.2 1.0 C25 A:X1D501 1.3 72.7 1.0 F1 A:X1D501 2.1 78.5 1.0 F3 A:X1D501 2.2 76.0 1.0 C24 A:X1D501 2.4 79.7 1.0 F6 A:X1D501 2.7 79.5 1.0 O4 A:X1D501 2.7 66.2 1.0 C26 A:X1D501 2.9 92.3 1.0 CD2 A:LEU240 3.2 49.3 1.0 F5 A:X1D501 3.4 72.8 1.0 C23 A:X1D501 3.7 71.5 1.0 F4 A:X1D501 4.2 67.7 1.0 CD2 A:LEU206 4.4 79.2 1.0 C27 A:X1D501 4.4 79.8 1.0 CD1 A:ILE414 4.5 46.5 1.0 CZ A:PHE420 4.5 48.4 1.0 CE2 A:PHE420 4.6 54.0 1.0 C22 A:X1D501 4.6 71.4 1.0 CG A:LEU240 4.7 50.7 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:76.0 occ:1.00 F3 A:X1D501 0.0 76.0 1.0 C25 A:X1D501 1.3 72.7 1.0 F1 A:X1D501 2.2 78.5 1.0 F2 A:X1D501 2.2 72.2 1.0 C24 A:X1D501 2.4 79.7 1.0 C23 A:X1D501 2.8 71.5 1.0 O4 A:X1D501 2.9 66.2 1.0 C22 A:X1D501 3.3 71.4 1.0 C27 A:X1D501 3.6 79.8 1.0 C26 A:X1D501 3.7 92.3 1.0 CD2 A:LEU209 4.0 102.9 1.0 F5 A:X1D501 4.1 72.8 1.0 F6 A:X1D501 4.2 79.5 1.0 C21 A:X1D501 4.4 84.4 1.0 CB A:LEU209 4.5 98.2 1.0 C28 A:X1D501 4.6 81.3 1.0 F4 A:X1D501 4.8 67.7 1.0 CD2 A:LEU240 4.8 49.3 1.0 CG A:LEU209 4.9 90.8 1.0 C20 A:X1D501 4.9 91.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:67.7 occ:1.00 F4 A:X1D501 0.0 67.7 1.0 C26 A:X1D501 1.3 92.3 1.0 F6 A:X1D501 2.1 79.5 1.0 F5 A:X1D501 2.2 72.8 1.0 C24 A:X1D501 2.4 79.7 1.0 C23 A:X1D501 2.9 71.5 1.0 O4 A:X1D501 2.9 66.2 1.0 NE2 A:HIS407 3.2 54.2 1.0 C27 A:X1D501 3.2 79.8 1.0 CE1 A:HIS407 3.6 48.7 1.0 CD1 A:LEU411 3.6 60.0 1.0 C25 A:X1D501 3.7 72.7 1.0 C22 A:X1D501 3.8 71.4 1.0 C16 A:X1D501 4.0 73.8 1.0 C17 A:X1D501 4.0 65.9 1.0 OG A:SER247 4.0 56.2 1.0 F1 A:X1D501 4.1 78.5 1.0 F2 A:X1D501 4.2 72.2 1.0 C28 A:X1D501 4.3 81.3 1.0 CD2 A:HIS407 4.4 46.8 1.0 C21 A:X1D501 4.8 84.4 1.0 F3 A:X1D501 4.8 76.0 1.0 CG A:LEU411 4.9 49.2 1.0 CB A:SER247 4.9 37.0 1.0 CE A:MET425 4.9 45.8 1.0 ND1 A:HIS407 4.9 50.9 1.0 C20 A:X1D501 5.0 91.9 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:72.8 occ:1.00 F5 A:X1D501 0.0 72.8 1.0 C26 A:X1D501 1.3 92.3 1.0 F6 A:X1D501 2.1 79.5 1.0 F4 A:X1D501 2.2 67.7 1.0 C24 A:X1D501 2.4 79.7 1.0 F1 A:X1D501 2.5 78.5 1.0 C27 A:X1D501 2.7 79.8 1.0 C25 A:X1D501 2.9 72.7 1.0 C23 A:X1D501 2.9 71.5 1.0 F2 A:X1D501 3.4 72.2 1.0 O4 A:X1D501 3.6 66.2 1.0 OG A:SER247 3.8 56.2 1.0 CB A:MET243 3.8 44.0 1.0 C28 A:X1D501 4.0 81.3 1.0 F3 A:X1D501 4.1 76.0 1.0 C A:MET243 4.2 42.4 1.0 O A:MET243 4.3 42.0 1.0 C22 A:X1D501 4.3 71.4 1.0 CE2 A:PHE420 4.4 54.0 1.0 N A:ALA244 4.5 42.2 1.0 CA A:MET243 4.7 52.3 1.0 CB A:SER247 4.8 37.0 1.0 CA A:ALA244 4.8 50.9 1.0 CG A:MET243 4.9 49.6 1.0 CD2 A:LEU240 5.0 49.3 1.0 CZ A:PHE420 5.0 48.4 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Pregnane X Receptor Ligand Binding Domain Complexed with T0901317 Analog Sjpyt-318


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 Sjpyt-318 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:79.5 occ:1.00 F6 A:X1D501 0.0 79.5 1.0 C26 A:X1D501 1.3 92.3 1.0 F5 A:X1D501 2.1 72.8 1.0 F4 A:X1D501 2.1 67.7 1.0 C24 A:X1D501 2.4 79.7 1.0 F2 A:X1D501 2.7 72.2 1.0 O4 A:X1D501 2.8 66.2 1.0 C25 A:X1D501 2.9 72.7 1.0 F1 A:X1D501 3.3 78.5 1.0 CD1 A:LEU411 3.4 60.0 1.0 CE2 A:PHE420 3.4 54.0 1.0 CZ A:PHE420 3.5 48.4 1.0 C23 A:X1D501 3.7 71.5 1.0 CG A:LEU411 4.1 49.2 1.0 F3 A:X1D501 4.2 76.0 1.0 NE2 A:HIS407 4.2 54.2 1.0 C27 A:X1D501 4.2 79.8 1.0 CD2 A:LEU240 4.5 49.3 1.0 CE A:MET425 4.7 45.8 1.0 CD2 A:PHE420 4.8 47.9 1.0 CE1 A:PHE420 4.8 45.5 1.0 CB A:LEU411 4.8 42.4 1.0 C22 A:X1D501 4.8 71.4 1.0 CE1 A:HIS407 4.8 48.7 1.0

A.D.Huber, S.Poudel, Y.Li, W.Lin, J.Wu, D.J.Miller, T.Chen. Ligand Flexibility and Binding Pocket Malleability Cooperate to Allow Selective Pxr Activation By Analogs of A Promiscuous Nuclear Receptor Ligand. Structure 2023.
ISSN: ISSN 0969-2126
PubMed: 37729916
DOI: 10.1016/J.STR.2023.08.020