Fluorine in PDB 7axd: Crystal Structure of the Hpxr-Lbd in Complex with Fipronil

The structure of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil, PDB code: 7axd was solved by M.Granell, V.Delfosse, W.Bourguet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.15 / 2.65
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.012, 92.012, 86.555, 90, 90, 90
R / Rfree (%)	19.5 / 23.7

The structure of Crystal Structure of the Hpxr-Lbd in Complex with Fipronil also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil (pdb code 7axd). 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 the Hpxr-Lbd in Complex with Fipronil, PDB code: 7axd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:70.4 occ:0.46 F A:S6W501 0.0 70.4 0.5 C10 A:S6W501 1.3 74.9 0.4 F1 A:S6W501 2.2 77.8 0.7 F2 A:S6W501 2.2 74.2 0.6 OG A:SER247 2.5 60.5 1.0 S A:S6W501 2.5 80.6 0.6 C7 A:S6W501 2.8 72.6 0.7 N2 A:S6W501 2.8 62.1 0.8 C9 A:S6W501 3.0 56.4 0.8 C8 A:S6W501 3.0 64.4 0.8 CB A:SER247 3.1 38.9 1.0 CZ A:PHE251 3.6 48.3 1.0 O A:S6W501 3.8 86.9 0.9 C6 A:S6W501 3.8 74.9 1.0 CE2 A:PHE251 4.0 46.7 1.0 N1 A:S6W501 4.1 70.2 0.7 CA A:SER247 4.3 48.7 1.0 N A:S6W501 4.5 63.5 1.0 CE1 A:PHE251 4.5 46.2 1.0 N3 A:S6W501 4.6 74.5 1.0 SG A:CYS284 4.8 64.5 1.0 CD1 A:PHE281 4.8 60.1 1.0 O2 A:IPA504 4.9 72.4 1.0 CL A:S6W501 5.0 66.8 0.7

Fluorine binding site 2 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:77.8 occ:0.65 F1 A:S6W501 0.0 77.8 0.7 C10 A:S6W501 1.3 74.9 0.4 F A:S6W501 2.2 70.4 0.5 F2 A:S6W501 2.2 74.2 0.6 S A:S6W501 2.5 80.6 0.6 O A:S6W501 3.0 86.9 0.9 O2 A:IPA504 3.0 72.4 1.0 OG A:SER247 3.2 60.5 1.0 C2 A:IPA504 3.2 86.0 1.0 C7 A:S6W501 3.5 72.6 0.7 C3 A:IPA504 3.6 72.8 1.0 CB A:SER247 4.0 38.9 1.0 C6 A:S6W501 4.1 74.9 1.0 N3 A:S6W501 4.2 74.5 1.0 C8 A:S6W501 4.4 64.4 0.8 C1 A:IPA504 4.6 63.1 1.0 CE A:MET425 4.6 45.2 1.0 N2 A:S6W501 4.7 62.1 0.8 C9 A:S6W501 4.8 56.4 0.8

Fluorine binding site 3 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:74.2 occ:0.60 F2 A:S6W501 0.0 74.2 0.6 C10 A:S6W501 1.3 74.9 0.4 F1 A:S6W501 2.2 77.8 0.7 F A:S6W501 2.2 70.4 0.5 S A:S6W501 2.6 80.6 0.6 O A:S6W501 3.5 86.9 0.9 N2 A:S6W501 3.6 62.1 0.8 C7 A:S6W501 3.9 72.6 0.7 CE2 A:PHE429 4.0 89.9 1.0 CZ A:PHE429 4.0 84.3 1.0 CD1 A:PHE281 4.1 60.1 1.0 CZ A:PHE251 4.3 48.3 1.0 C9 A:S6W501 4.3 56.4 0.8 OG A:SER247 4.4 60.5 1.0 C8 A:S6W501 4.5 64.4 0.8 CE1 A:PHE281 4.5 58.8 1.0 CE2 A:PHE251 4.7 46.7 1.0 CB A:SER247 5.0 38.9 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:65.2 occ:0.63 F3 A:S6W501 0.0 65.2 0.6 C11 A:S6W501 1.3 59.1 0.8 F5 A:S6W501 2.2 61.2 0.6 F4 A:S6W501 2.2 57.5 0.6 C1 A:S6W501 2.3 68.6 0.9 C2 A:S6W501 3.0 73.3 1.0 CB A:TYR306 3.1 42.9 1.0 CG A:TYR306 3.1 53.9 1.0 C A:S6W501 3.2 62.3 0.9 CD2 A:TYR306 3.4 54.5 1.0 CE A:MET243 3.7 76.2 1.0 CD1 A:TYR306 3.8 46.0 1.0 C2 A:IPA505 3.9 82.4 1.0 CE3 A:TRP299 3.9 51.1 1.0 C1 A:IPA505 4.0 78.8 1.0 CE2 A:TYR306 4.2 57.0 1.0 C3 A:S6W501 4.2 71.0 0.8 C5 A:S6W501 4.3 69.2 0.8 CD2 A:TRP299 4.4 56.1 1.0 CG1 A:VAL211 4.5 54.2 1.0 CZ3 A:TRP299 4.5 51.0 1.0 CE1 A:TYR306 4.5 48.2 1.0 O2 A:IPA505 4.6 80.7 1.0 CA A:TYR306 4.6 55.0 1.0 CG2 A:VAL211 4.6 73.7 1.0 CB A:TRP299 4.6 44.4 1.0 SD A:MET243 4.6 85.9 1.0 CG A:TRP299 4.7 52.9 1.0 CZ A:TYR306 4.7 57.7 1.0 C4 A:S6W501 4.7 66.8 0.9 CB A:VAL211 5.0 60.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:57.5 occ:0.57 F4 A:S6W501 0.0 57.5 0.6 C11 A:S6W501 1.3 59.1 0.8 F5 A:S6W501 2.2 61.2 0.6 F3 A:S6W501 2.2 65.2 0.6 C1 A:S6W501 2.3 68.6 0.9 C2 A:S6W501 2.8 73.3 1.0 CB A:TRP299 3.0 44.4 1.0 CG A:TRP299 3.3 52.9 1.0 C A:S6W501 3.4 62.3 0.9 CD1 A:TYR306 3.4 46.0 1.0 CG A:TYR306 3.5 53.9 1.0 CB A:TYR306 3.6 42.9 1.0 CD2 A:TRP299 3.7 56.1 1.0 CE3 A:TRP299 3.9 51.1 1.0 CE1 A:PHE288 4.0 58.0 1.0 CD1 A:PHE288 4.1 56.6 1.0 C3 A:S6W501 4.1 71.0 0.8 CD1 A:TRP299 4.1 45.3 1.0 CE1 A:TYR306 4.1 48.2 1.0 SG A:CYS301 4.2 44.5 1.0 CD2 A:TYR306 4.3 54.5 1.0 CA A:TRP299 4.4 54.0 1.0 C5 A:S6W501 4.5 69.2 0.8 O A:TRP299 4.6 47.6 1.0 CE2 A:TRP299 4.6 62.5 1.0 C4 A:S6W501 4.8 66.8 0.9 CZ A:PHE288 4.8 64.5 1.0 C A:TRP299 4.8 45.6 1.0 NE1 A:TRP299 4.8 52.1 1.0 CZ A:TYR306 4.8 57.7 1.0 CE2 A:TYR306 4.9 57.0 1.0 CZ3 A:TRP299 4.9 51.0 1.0 CA A:TYR306 5.0 55.0 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the Hpxr-Lbd in Complex with Fipronil


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 Hpxr-Lbd in Complex with Fipronil within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:61.2 occ:0.56 F5 A:S6W501 0.0 61.2 0.6 C11 A:S6W501 1.3 59.1 0.8 F4 A:S6W501 2.2 57.5 0.6 F3 A:S6W501 2.2 65.2 0.6 C1 A:S6W501 2.3 68.6 0.9 C A:S6W501 2.5 62.3 0.9 CD1 A:TYR306 2.9 46.0 1.0 CG A:TYR306 2.9 53.9 1.0 CE1 A:TYR306 3.0 48.2 1.0 CD2 A:TYR306 3.1 54.5 1.0 CZ A:TYR306 3.2 57.7 1.0 CE2 A:TYR306 3.2 57.0 1.0 C2 A:S6W501 3.5 73.3 1.0 CB A:TYR306 3.8 42.9 1.0 C5 A:S6W501 3.8 69.2 0.8 CE A:MET243 4.0 76.2 1.0 OH A:TYR306 4.1 46.4 1.0 SD A:MET243 4.4 85.9 1.0 CE1 A:PHE288 4.4 58.0 1.0 CG A:MET246 4.5 44.2 1.0 C3 A:S6W501 4.5 71.0 0.8 C4 A:S6W501 4.6 66.8 0.9 CE A:MET246 4.7 39.9 1.0 SG A:CYS301 4.7 44.5 1.0 CZ A:PHE288 4.8 64.5 1.0 CL A:S6W501 4.8 66.8 0.7 CB A:TRP299 5.0 44.4 1.0

V.Delfosse, T.Huet, D.Harrus, M.Granell, M.Bourguet, C.Gardia-Parege, B.Chiavarina, M.Grimaldi, S.Le Mevel, P.Blanc, D.Huang, J.Gruszczyk, B.Demeneix, S.Cianferani, J.B.Fini, P.Balaguer, W.Bourguet. Mechanistic Insights Into the Synergistic Activation of the Rxr-Pxr Heterodimer By Endocrine Disruptor Mixtures. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33361153
DOI: 10.1073/PNAS.2020551118