Fluorine in PDB 7riv: Human Pxr Lbd Bound to GSK001

The structure of Human Pxr Lbd Bound to GSK001, PDB code: 7riv was solved by S.P.Williams, G.B.Wisely, P.Ward, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.32 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.559, 91.559, 85.17, 90, 90, 90
R / Rfree (%)	19 / 23.8

The binding sites of Fluorine atom in the Human Pxr Lbd Bound to GSK001 (pdb code 7riv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Pxr Lbd Bound to GSK001, PDB code: 7riv:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human Pxr Lbd Bound to GSK001


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Pxr Lbd Bound to GSK001 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:41.7 occ:1.00 F39 A:P06501 0.0 41.7 1.0 C32 A:P06501 1.4 42.7 1.0 C30 A:P06501 2.4 41.5 1.0 C31 A:P06501 2.4 41.5 1.0 N40 A:P06501 2.7 40.9 1.0 C16 A:P06501 2.8 42.5 1.0 C2 A:P06501 2.9 44.9 1.0 C12 A:P06501 3.0 39.8 1.0 F53 A:P06501 3.0 36.5 1.0 OG A:SER247 3.1 34.0 1.0 N3 A:P06501 3.2 46.1 1.0 C46 A:P06501 3.4 40.4 1.0 C4 A:P06501 3.4 50.4 1.0 C35 A:P06501 3.6 43.4 1.0 C33 A:P06501 3.6 41.7 1.0 C43 A:P06501 3.8 39.7 1.0 CE A:MET243 3.8 48.3 1.0 C1 A:P06501 3.8 46.9 1.0 S42 A:P06501 3.9 38.5 1.0 N15 A:P06501 4.0 41.9 1.0 C7 A:P06501 4.1 51.2 1.0 C44 A:P06501 4.1 39.0 1.0 C37 A:P06501 4.1 41.5 1.0 N6 A:P06501 4.3 52.4 1.0 CB A:MET243 4.3 24.8 1.0 O A:MET243 4.5 26.4 1.0 S13 A:P06501 4.5 41.3 1.0 CB A:SER247 4.5 26.1 1.0 C14 A:P06501 4.7 44.9 1.0 N9 A:P06501 4.7 49.7 1.0 CG A:MET243 4.8 34.3 1.0 C49 A:P06501 4.8 43.0 1.0 O54 A:P06501 4.8 41.2 1.0 O55 A:P06501 4.9 34.8 1.0 C A:MET243 5.0 27.1 1.0

Fluorine binding site 2 out of 3 in the Human Pxr Lbd Bound to GSK001


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Pxr Lbd Bound to GSK001 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:41.4 occ:1.00 F52 A:P06501 0.0 41.4 1.0 C49 A:P06501 1.3 43.0 1.0 C50 A:P06501 2.4 41.7 1.0 C43 A:P06501 2.4 39.7 1.0 O54 A:P06501 2.5 41.2 1.0 S42 A:P06501 3.0 38.5 1.0 C47 A:P06501 3.6 39.6 1.0 C46 A:P06501 3.6 40.4 1.0 O A:HIS407 3.6 31.4 1.0 CD2 A:PHE281 3.7 32.2 1.0 CE2 A:PHE281 3.8 28.3 1.0 CB A:HIS407 3.8 32.0 1.0 O55 A:P06501 3.8 34.8 1.0 CZ A:PHE429 3.9 43.0 1.0 C A:HIS407 4.0 32.0 1.0 CD1 A:LEU411 4.0 37.7 1.0 N9 A:P06501 4.1 49.7 1.0 C44 A:P06501 4.1 39.0 1.0 CB A:LEU411 4.2 34.2 1.0 N40 A:P06501 4.3 40.9 1.0 CE2 A:PHE429 4.3 36.8 1.0 ND1 A:HIS407 4.4 46.3 1.0 CA A:HIS407 4.5 32.2 1.0 C31 A:P06501 4.5 41.5 1.0 CG A:HIS407 4.6 37.6 1.0 N A:THR408 4.6 29.9 1.0 C33 A:P06501 4.7 41.7 1.0 F53 A:P06501 4.7 36.5 1.0 CG A:LEU411 4.8 37.4 1.0 CG A:PHE281 4.9 23.9 1.0 CE1 A:PHE429 4.9 38.5 1.0 CZ A:PHE281 5.0 32.6 1.0 C1 A:P06501 5.0 46.9 1.0

Fluorine binding site 3 out of 3 in the Human Pxr Lbd Bound to GSK001


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Pxr Lbd Bound to GSK001 within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:36.5 occ:1.00 F53 A:P06501 0.0 36.5 1.0 C46 A:P06501 1.3 40.4 1.0 C43 A:P06501 2.3 39.7 1.0 C44 A:P06501 2.4 39.0 1.0 N40 A:P06501 2.6 40.9 1.0 S42 A:P06501 2.9 38.5 1.0 F39 A:P06501 3.0 41.7 1.0 O55 A:P06501 3.1 34.8 1.0 C31 A:P06501 3.5 41.5 1.0 OG A:SER247 3.5 34.0 1.0 C47 A:P06501 3.6 39.6 1.0 C49 A:P06501 3.6 43.0 1.0 CE A:MET425 3.7 27.0 1.0 C32 A:P06501 3.7 42.7 1.0 CE2 A:PHE420 4.1 32.0 1.0 C50 A:P06501 4.1 41.7 1.0 CD1 A:LEU411 4.2 37.7 1.0 O54 A:P06501 4.3 41.2 1.0 CB A:SER247 4.4 26.1 1.0 CZ A:PHE420 4.6 33.2 1.0 O A:MET243 4.6 26.4 1.0 F52 A:P06501 4.7 41.4 1.0 CB A:MET243 4.8 24.8 1.0 C33 A:P06501 4.8 41.7 1.0 C1 A:P06501 4.8 46.9 1.0 C A:MET243 4.8 27.1 1.0 N6 A:P06501 4.9 52.4 1.0 N3 A:P06501 4.9 46.1 1.0

J.M.Ramajulu, S.P.Williams, A.S.Lakdawala, M.P.Demartino, Y.Lan, R.W.Marquis. Overcoming the Pxr Liability: Rationale Design to Eliminate Pxr Mediated Cyp Induction Acs Med.Chem.Lett. V. 12 2021.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.1C00187