Fluorine in PDB 2o9i: Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317

The structure of Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317, PDB code: 2o9i was solved by Y.Xue, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.979, 90.618, 105.725, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 24

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 (pdb code 2o9i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317, PDB code: 2o9i:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:92.5 occ:1.00 F22 A:4442 0.0 92.5 1.0 C19 A:4442 1.4 91.7 1.0 F20 A:4442 2.2 92.7 1.0 F21 A:4442 2.2 92.3 1.0 C16 A:4442 2.4 91.2 1.0 O A:LEU209 2.8 52.1 1.0 CB A:LEU209 3.0 57.1 1.0 C24 A:4442 3.1 84.1 1.0 CA A:LEU209 3.3 54.9 1.0 N15 A:4442 3.3 91.1 1.0 C A:LEU209 3.4 52.7 1.0 C23 A:4442 3.5 87.5 1.0 CG A:LEU209 3.9 59.2 1.0 CD1 A:LEU209 4.0 58.9 1.0 C25 A:4442 4.0 82.4 1.0 CD2 A:LEU209 4.0 57.7 1.0 CG1 A:VAL211 4.4 40.3 1.0 C28 A:4442 4.6 86.3 1.0 S12 A:4442 4.7 95.5 1.0 N A:LYS210 4.7 49.2 1.0 N A:LEU209 4.8 57.0 1.0

Fluorine binding site 2 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:92.3 occ:1.00 F21 A:4442 0.0 92.3 1.0 C19 A:4442 1.4 91.7 1.0 F22 A:4442 2.2 92.5 1.0 F20 A:4442 2.2 92.7 1.0 C16 A:4442 2.4 91.2 1.0 N15 A:4442 3.0 91.1 1.0 CD2 A:LEU209 3.0 57.7 1.0 CB A:LEU209 3.6 57.1 1.0 C23 A:4442 3.6 87.5 1.0 CG A:LEU209 3.7 59.2 1.0 CA A:LEU209 3.8 54.9 1.0 CD2 A:LEU324 3.9 45.9 1.0 CD1 A:LEU209 4.0 58.9 1.0 C24 A:4442 4.1 84.1 1.0 O A:LEU209 4.3 52.1 1.0 S12 A:4442 4.4 95.5 1.0 C28 A:4442 4.5 86.3 1.0 C A:LEU209 4.5 52.7 1.0 CH2 A:TRP299 4.5 40.9 1.0 O13 A:4442 4.6 95.7 1.0 SD A:MET323 4.6 57.2 1.0 O A:SER208 4.7 58.4 1.0 CB A:MET323 4.8 50.2 1.0 CZ3 A:TRP299 4.9 38.9 1.0 N A:LEU209 5.0 57.0 1.0

Fluorine binding site 3 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:92.7 occ:1.00 F20 A:4442 0.0 92.7 1.0 C19 A:4442 1.4 91.7 1.0 F22 A:4442 2.2 92.5 1.0 F21 A:4442 2.2 92.3 1.0 C16 A:4442 2.4 91.2 1.0 O A:LEU209 3.2 52.1 1.0 CZ3 A:TRP299 3.5 38.9 1.0 CG1 A:VAL211 3.5 40.3 1.0 CD1 A:LEU308 3.7 58.4 1.0 CA A:LEU209 3.7 54.9 1.0 CH2 A:TRP299 3.7 40.9 1.0 C A:LEU209 3.8 52.7 1.0 N15 A:4442 3.8 91.1 1.0 CB A:LEU209 4.2 57.1 1.0 CD2 A:LEU324 4.3 45.9 1.0 CE3 A:TRP299 4.5 38.4 1.0 CD2 A:LEU209 4.6 57.7 1.0 C23 A:4442 4.7 87.5 1.0 S12 A:4442 4.7 95.5 1.0 C24 A:4442 4.7 84.1 1.0 O13 A:4442 4.8 95.7 1.0 CG A:LEU308 4.9 56.7 1.0 CB A:VAL211 4.9 41.1 1.0 CZ2 A:TRP299 4.9 38.4 1.0 N A:LYS210 4.9 49.2 1.0 O A:SER208 5.0 58.4 1.0 O A:LYS210 5.0 43.3 1.0 CG A:LEU209 5.0 59.2 1.0

Fluorine binding site 4 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:81.6 occ:1.00 F36 A:4442 0.0 81.6 1.0 C34 A:4442 1.3 80.8 1.0 F37 A:4442 2.2 79.8 1.0 F35 A:4442 2.2 82.2 1.0 C33 A:4442 2.4 79.8 1.0 O42 A:4442 2.8 79.5 1.0 F39 A:4442 2.9 78.2 1.0 C38 A:4442 3.1 77.9 1.0 CE1 A:PHE420 3.1 45.5 1.0 CD1 A:LEU411 3.4 44.5 1.0 CZ A:PHE420 3.4 46.7 1.0 CE A:MET425 3.5 44.3 1.0 F41 A:4442 3.6 76.3 1.0 C26 A:4442 3.9 81.6 1.0 F40 A:4442 4.3 75.7 1.0 CG A:LEU411 4.4 44.9 1.0 CD1 A:PHE420 4.4 45.7 1.0 C25 A:4442 4.7 82.4 1.0 CE2 A:PHE420 4.8 47.4 1.0 C27 A:4442 5.0 83.5 1.0 CD2 A:LEU240 5.0 35.8 1.0

Fluorine binding site 5 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:79.8 occ:1.00 F37 A:4442 0.0 79.8 1.0 C34 A:4442 1.3 80.8 1.0 F36 A:4442 2.2 81.6 1.0 F35 A:4442 2.2 82.2 1.0 C33 A:4442 2.4 79.8 1.0 F41 A:4442 2.9 76.3 1.0 C38 A:4442 3.1 77.9 1.0 C26 A:4442 3.2 81.6 1.0 CB A:MET243 3.2 33.1 1.0 C25 A:4442 3.3 82.4 1.0 O42 A:4442 3.6 79.5 1.0 F39 A:4442 3.6 78.2 1.0 CG A:MET243 4.1 36.4 1.0 C A:MET243 4.2 34.5 1.0 CE1 A:PHE420 4.2 45.5 1.0 F40 A:4442 4.3 75.7 1.0 CA A:MET243 4.3 34.0 1.0 N A:ALA244 4.4 35.0 1.0 C27 A:4442 4.6 83.5 1.0 O A:MET243 4.6 33.8 1.0 CD2 A:LEU240 4.6 35.8 1.0 C24 A:4442 4.6 84.1 1.0 O A:LEU240 4.8 39.1 1.0 CZ A:PHE420 4.9 46.7 1.0 CE A:MET425 4.9 44.3 1.0 SD A:MET243 4.9 39.3 1.0 CA A:ALA244 5.0 36.1 1.0

Fluorine binding site 6 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:82.2 occ:1.00 F35 A:4442 0.0 82.2 1.0 C34 A:4442 1.4 80.8 1.0 F37 A:4442 2.2 79.8 1.0 F36 A:4442 2.2 81.6 1.0 C33 A:4442 2.4 79.8 1.0 O42 A:4442 2.8 79.5 1.0 C26 A:4442 3.0 81.6 1.0 C25 A:4442 3.8 82.4 1.0 C27 A:4442 3.8 83.5 1.0 CB A:SER247 3.8 39.1 1.0 C38 A:4442 3.8 77.9 1.0 CE A:MET425 4.0 44.3 1.0 OG A:SER247 4.0 42.9 1.0 F39 A:4442 4.4 78.2 1.0 F41 A:4442 4.4 76.3 1.0 O A:HOH3025 4.4 45.1 1.0 CD1 A:LEU411 4.6 44.5 1.0 NE2 A:HIS407 4.6 47.0 1.0 O A:MET243 4.7 33.8 1.0 CB A:MET243 4.8 33.1 1.0 F40 A:4442 4.8 75.7 1.0 C24 A:4442 4.9 84.1 1.0 C28 A:4442 4.9 86.3 1.0 C A:MET243 4.9 34.5 1.0

Fluorine binding site 7 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:78.2 occ:1.00 F39 A:4442 0.0 78.2 1.0 C38 A:4442 1.3 77.9 1.0 F40 A:4442 2.1 75.7 1.0 F41 A:4442 2.2 76.3 1.0 C33 A:4442 2.5 79.8 1.0 O42 A:4442 2.8 79.5 1.0 F36 A:4442 2.9 81.6 1.0 C34 A:4442 3.1 80.8 1.0 F37 A:4442 3.6 79.8 1.0 CD1 A:ILE414 3.7 42.0 1.0 CZ A:PHE420 3.8 46.7 1.0 C26 A:4442 3.8 81.6 1.0 CD1 A:LEU411 4.1 44.5 1.0 CD2 A:LEU240 4.1 35.8 1.0 CE1 A:PHE420 4.3 45.5 1.0 CG A:LEU411 4.3 44.9 1.0 F35 A:4442 4.4 82.2 1.0 CB A:LEU411 4.5 43.0 1.0 CD2 A:LEU206 4.6 53.0 1.0 C25 A:4442 4.6 82.4 1.0 CA A:LEU411 4.7 41.8 1.0 CE2 A:PHE420 4.7 47.4 1.0 NE2 A:HIS407 4.8 47.0 1.0 C27 A:4442 4.9 83.5 1.0 CG1 A:ILE414 4.9 43.2 1.0

Fluorine binding site 8 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:75.7 occ:1.00 F40 A:4442 0.0 75.7 1.0 C38 A:4442 1.4 77.9 1.0 F41 A:4442 2.1 76.3 1.0 F39 A:4442 2.1 78.2 1.0 C33 A:4442 2.4 79.8 1.0 O42 A:4442 2.8 79.5 1.0 C26 A:4442 2.9 81.6 1.0 C25 A:4442 3.6 82.4 1.0 C27 A:4442 3.6 83.5 1.0 CD1 A:LEU209 3.9 58.9 1.0 C34 A:4442 3.9 80.8 1.0 NE2 A:HIS407 4.3 47.0 1.0 F37 A:4442 4.3 79.8 1.0 CD1 A:ILE414 4.3 42.0 1.0 F36 A:4442 4.3 81.6 1.0 CD A:ARG410 4.4 36.4 1.0 CD2 A:LEU206 4.5 53.0 1.0 CD2 A:HIS407 4.5 44.9 1.0 C24 A:4442 4.6 84.1 1.0 C28 A:4442 4.7 86.3 1.0 F35 A:4442 4.8 82.2 1.0

Fluorine binding site 9 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ A:F2 b:76.3 occ:1.00 F41 A:4442 0.0 76.3 1.0 C38 A:4442 1.3 77.9 1.0 F40 A:4442 2.1 75.7 1.0 F39 A:4442 2.2 78.2 1.0 C33 A:4442 2.5 79.8 1.0 F37 A:4442 2.9 79.8 1.0 C34 A:4442 3.1 80.8 1.0 C26 A:4442 3.1 81.6 1.0 C25 A:4442 3.2 82.4 1.0 CD2 A:LEU240 3.6 35.8 1.0 O42 A:4442 3.6 79.5 1.0 F36 A:4442 3.6 81.6 1.0 CD2 A:LEU206 3.9 53.0 1.0 F35 A:4442 4.4 82.2 1.0 C24 A:4442 4.5 84.1 1.0 C27 A:4442 4.5 83.5 1.0 CD1 A:ILE414 4.7 42.0 1.0

Fluorine binding site 10 out of 18 in the Crystal Structure of the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317


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 the Human Pregnane X Receptor Lbd in Complex with An Src-1 Coactivator Peptide and T0901317 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:91.8 occ:1.00 F22 B:4441 0.0 91.8 1.0 C19 B:4441 1.4 91.1 1.0 F21 B:4441 2.2 92.3 1.0 F20 B:4441 2.2 91.9 1.0 C16 B:4441 2.4 90.3 1.0 N15 B:4441 3.0 90.2 1.0 CD2 B:LEU1209 3.2 49.0 1.0 C23 B:4441 3.4 87.3 1.0 CB B:MET1323 3.4 48.7 1.0 CE B:MET1323 3.4 48.0 1.0 C24 B:4441 3.6 83.8 1.0 SD B:MET1323 3.7 52.4 1.0 CG B:MET1323 4.0 50.4 1.0 CG B:LEU1209 4.1 50.4 1.0 CD1 B:LEU1209 4.1 50.0 1.0 C28 B:4441 4.4 84.5 1.0 CD2 B:LEU1324 4.4 46.8 1.0 CB B:LEU1209 4.4 52.1 1.0 S12 B:4441 4.5 92.3 1.0 CA B:MET1323 4.6 45.8 1.0 C25 B:4441 4.6 82.0 1.0 C B:MET1323 4.6 45.2 1.0 CD1 B:LEU1324 4.9 46.9 1.0 O B:MET1323 4.9 43.6 1.0 O13 B:4441 4.9 92.3 1.0 OE1 B:GLN1285 5.0 45.6 1.0

Y.Xue, E.Chao, W.J.Zuercher, T.M.Willson, J.L.Collins, M.R.Redinbo. Crystal Structure of the Pxr-T1317 Complex Provides A Scaffold to Examine the Potential For Receptor Antagonism. Bioorg.Med.Chem. V. 15 2156 2007.
ISSN: ISSN 0968-0896
PubMed: 17215127
DOI: 10.1016/J.BMC.2006.12.026