Fluorine in PDB 6s41: Crystal Structure of Pxr in Complex with Xpc-7455

The structure of Crystal Structure of Pxr in Complex with Xpc-7455, PDB code: 6s41 was solved by T.Focken, K.Maskos, A.Griessner, S.Krapp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.11 / 2.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.318, 89.002, 105.815, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.9

The structure of Crystal Structure of Pxr in Complex with Xpc-7455 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Pxr in Complex with Xpc-7455 (pdb code 6s41). 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 Pxr in Complex with Xpc-7455, PDB code: 6s41:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:75.1 occ:1.00 F22 A:KUB701 0.0 75.1 1.0 C21 A:KUB701 1.3 60.5 1.0 C20 A:KUB701 2.4 60.3 1.0 C23 A:KUB701 2.4 56.8 1.0 CD2 A:LEU324 3.4 38.2 1.0 CG A:MET323 3.5 50.8 1.0 C19 A:KUB701 3.6 58.5 1.0 C24 A:KUB701 3.7 54.4 1.0 CD2 A:LEU209 3.7 70.3 1.0 CE A:MET323 3.8 55.1 1.0 SD A:MET323 3.8 52.0 1.0 CH2 A:TRP299 3.9 27.1 1.0 CZ2 A:TRP299 4.0 26.8 1.0 CB A:MET323 4.1 44.8 1.0 C25 A:KUB701 4.1 55.0 1.0 CG A:LEU324 4.4 38.6 1.0 C A:MET323 4.4 35.4 1.0 O A:MET323 4.4 36.7 1.0 CD2 A:HIS327 4.5 25.0 1.0 N A:LEU324 4.6 34.9 1.0 CG A:LEU209 4.7 72.0 1.0 CD1 A:LEU209 4.8 77.0 1.0 CA A:LEU324 4.8 35.5 1.0 NE2 A:HIS327 4.9 24.4 1.0 C16 A:KUB701 4.9 54.5 1.0 CA A:MET323 4.9 38.7 1.0 CZ3 A:TRP299 4.9 26.6 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:61.4 occ:1.00 F26 A:KUB701 0.0 61.4 1.0 C25 A:KUB701 1.3 55.0 1.0 C24 A:KUB701 2.4 54.4 1.0 C19 A:KUB701 2.4 58.5 1.0 N15 A:KUB701 2.8 57.3 1.0 C16 A:KUB701 2.9 54.5 1.0 CE A:MET243 3.2 56.8 1.0 C18 A:KUB701 3.3 54.6 1.0 C14 A:KUB701 3.6 54.0 1.0 C23 A:KUB701 3.6 56.8 1.0 C20 A:KUB701 3.7 60.3 1.0 C21 A:KUB701 4.1 60.5 1.0 SD A:MET243 4.1 54.4 1.0 C12 A:KUB701 4.3 57.9 1.0 CG A:TYR306 4.3 27.6 1.0 CL1 A:KUB701 4.3 60.8 1.0 CG2 A:VAL211 4.4 31.8 1.0 C27 A:KUB701 4.4 48.7 1.0 CB A:TYR306 4.4 26.8 1.0 CD2 A:TYR306 4.4 31.3 1.0 CG1 A:VAL211 4.5 35.6 1.0 CE3 A:TRP299 4.8 26.9 1.0 CD1 A:TYR306 4.8 29.4 1.0 CZ3 A:TRP299 4.8 26.6 1.0 CE2 A:TYR306 5.0 32.1 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ A:F701 b:57.9 occ:1.00 F29 A:KUB701 0.0 57.9 1.0 C28 A:KUB701 1.3 51.8 1.0 C27 A:KUB701 2.4 48.7 1.0 C10 A:KUB701 2.4 51.4 1.0 O3 A:KUB701 2.7 50.3 1.0 S2 A:KUB701 3.0 51.3 1.0 CE1 A:HIS407 3.0 36.5 1.0 NE2 A:GLN285 3.4 36.0 1.0 CE A:MET323 3.4 55.1 1.0 CE1 A:PHE281 3.4 23.7 1.0 NE2 A:HIS407 3.5 35.0 1.0 N4 A:KUB701 3.6 56.0 1.0 C11 A:KUB701 3.6 54.6 1.0 C14 A:KUB701 3.7 54.0 1.0 ND1 A:HIS407 3.8 38.1 1.0 CD1 A:PHE281 4.0 24.1 1.0 C12 A:KUB701 4.1 57.9 1.0 O1 A:KUB701 4.3 57.1 1.0 CD A:GLN285 4.4 31.1 1.0 C5 A:KUB701 4.4 65.1 1.0 CD2 A:HIS407 4.5 36.0 1.0 CZ A:PHE281 4.5 24.8 1.0 CG A:HIS407 4.6 35.0 1.0 SD A:MET323 4.7 52.0 1.0 OE1 A:GLN285 4.8 31.7 1.0 N9 A:KUB701 4.9 59.4 1.0 N15 A:KUB701 4.9 57.3 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:82.6 occ:1.00 F22 B:KUB701 0.0 82.6 1.0 C21 B:KUB701 1.4 69.7 1.0 C20 B:KUB701 2.4 62.0 1.0 C23 B:KUB701 2.4 65.0 1.0 CZ2 B:TRP299 3.5 18.6 1.0 CD2 B:HIS327 3.5 21.5 1.0 CE B:MET323 3.6 45.1 1.0 CG B:MET323 3.6 35.0 1.0 CD2 B:LEU324 3.6 35.5 1.0 CH2 B:TRP299 3.6 18.9 1.0 C24 B:KUB701 3.6 59.5 1.0 C19 B:KUB701 3.7 57.7 1.0 NE2 B:HIS327 4.0 21.4 1.0 O B:MET323 4.0 24.7 1.0 SD B:MET323 4.1 44.2 1.0 C25 B:KUB701 4.1 59.6 1.0 C B:MET323 4.2 25.0 1.0 CB B:MET323 4.3 29.7 1.0 CD2 B:LEU209 4.4 36.9 1.0 N B:LEU324 4.4 24.2 1.0 OE1 B:GLN285 4.5 24.9 1.0 CE2 B:TRP299 4.5 18.1 1.0 CG B:HIS327 4.5 20.9 1.0 CA B:LEU324 4.6 24.1 1.0 CG B:LEU324 4.6 31.6 1.0 CZ3 B:TRP299 4.7 19.3 1.0 C16 B:KUB701 4.9 59.6 1.0 CA B:MET323 4.9 26.3 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:66.8 occ:1.00 F26 B:KUB701 0.0 66.8 1.0 C25 B:KUB701 1.3 59.6 1.0 C24 B:KUB701 2.4 59.5 1.0 C19 B:KUB701 2.4 57.7 1.0 N15 B:KUB701 2.7 63.6 1.0 C16 B:KUB701 2.9 59.6 1.0 C18 B:KUB701 3.4 59.7 1.0 C23 B:KUB701 3.6 65.0 1.0 C14 B:KUB701 3.6 74.1 1.0 C20 B:KUB701 3.7 62.0 1.0 SD B:MET243 3.7 48.5 1.0 C21 B:KUB701 4.1 69.7 1.0 CE B:MET243 4.2 41.7 1.0 CG2 B:VAL211 4.2 29.6 1.0 C27 B:KUB701 4.2 71.1 1.0 CG1 B:VAL211 4.3 29.7 1.0 C12 B:KUB701 4.5 83.5 1.0 CB B:TYR306 4.7 28.5 1.0 CZ3 B:TRP299 4.7 19.3 1.0 CE3 B:TRP299 4.7 19.0 1.0 CL1 B:KUB701 4.8 86.8 1.0 CG B:TYR306 4.8 30.0 1.0 CB B:VAL211 4.9 28.9 1.0 O B:LEU209 5.0 33.8 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Pxr in Complex with Xpc-7455


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 Pxr in Complex with Xpc-7455 within 5.0Å range: probe atom residue distance (Å) B Occ B:F701 b:58.5 occ:1.00 F29 B:KUB701 0.0 58.5 1.0 C28 B:KUB701 1.3 74.3 1.0 C27 B:KUB701 2.4 71.1 1.0 C10 B:KUB701 2.4 84.2 1.0 O3 B:KUB701 2.7 81.7 1.0 S2 B:KUB701 2.9 81.6 1.0 NE2 B:HIS407 3.2 45.4 1.0 CE B:MET323 3.4 45.1 1.0 CE1 B:PHE281 3.4 19.1 1.0 N4 B:KUB701 3.5 88.5 1.0 C11 B:KUB701 3.6 83.4 1.0 C14 B:KUB701 3.7 74.1 1.0 NE2 B:GLN285 3.7 28.4 1.0 CD2 B:HIS407 3.8 39.9 1.0 CD1 B:PHE281 4.0 22.0 1.0 CE1 B:HIS407 4.1 46.2 1.0 C5 B:KUB701 4.1 90.1 1.0 C12 B:KUB701 4.1 83.5 1.0 N9 B:KUB701 4.2 90.1 1.0 O1 B:KUB701 4.3 93.5 1.0 SD B:MET323 4.5 44.2 1.0 CZ B:PHE281 4.5 20.4 1.0 CD B:GLN285 4.7 25.7 1.0 CG B:HIS407 4.8 38.4 1.0 N15 B:KUB701 4.8 63.6 1.0 ND1 B:HIS407 4.9 45.2 1.0

T.Focken, K.Burford, M.E.Grimwood, A.Zenova, J.C.Andrez, W.Gong, M.Wilson, M.Taron, S.Decker, V.Lofstrand, S.Chowdhury, N.Shuart, S.Lin, S.J.Goodchild, C.Young, M.Soriano, P.K.Tari, M.Waldbrook, K.Nelkenbrecher, R.Kwan, A.Lindgren, G.De Boer, S.Lee, L.Sojo, R.J.Devita, C.J.Cohen, S.S.Wesolowski, J.P.Johnson Jr., C.M.Dehnhardt, J.R.Empfield. Identification of Cns-Penetrant Aryl Sulfonamides As Isoform-Selective NAV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy. J.Med.Chem. V. 62 9618 2019.
ISSN: ISSN 0022-2623
PubMed: 31525968
DOI: 10.1021/ACS.JMEDCHEM.9B01032