Fluorine in PDB 7nbw: Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist

The structure of Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist, PDB code: 7nbw was solved by S.Schmelz, W.Blankenfeldt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.62 / 2.28
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	121.386, 121.386, 114.839, 90, 90, 120
R / Rfree (%)	24.4 / 26.5

The binding sites of Fluorine atom in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist (pdb code 7nbw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist, PDB code: 7nbw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:79.8 occ:1.00 F01 A:U7Q401 0.0 79.8 1.0 C02 A:U7Q401 1.4 67.7 1.0 C07 A:U7Q401 2.4 62.9 1.0 C03 A:U7Q401 2.4 62.0 1.0 H071 A:U7Q401 2.6 76.4 1.0 H031 A:U7Q401 2.6 75.4 1.0 HD12 A:LEU189 2.6 89.0 1.0 HG21 A:VAL170 3.1 63.3 1.0 CD1 A:LEU189 3.3 73.3 1.0 HD13 A:LEU189 3.4 89.0 1.0 HD11 A:LEU189 3.6 89.0 1.0 C06 A:U7Q401 3.6 55.7 1.0 C04 A:U7Q401 3.6 58.0 1.0 HG13 A:ILE186 3.8 103.9 1.0 HD12 A:ILE186 3.8 80.9 1.0 HB A:ILE186 3.9 126.4 1.0 CG2 A:VAL170 4.0 52.0 1.0 HA A:ILE186 4.0 130.0 1.0 C05 A:U7Q401 4.1 51.2 1.0 HG22 A:VAL170 4.2 63.3 1.0 HG23 A:VAL170 4.3 63.3 1.0 HG11 A:VAL170 4.3 69.4 1.0 CG1 A:ILE186 4.4 85.8 1.0 H061 A:U7Q401 4.4 67.8 1.0 H041 A:U7Q401 4.4 70.5 1.0 HB2 A:LEU189 4.4 89.6 1.0 CB A:ILE186 4.5 104.6 1.0 CD1 A:ILE186 4.5 66.6 1.0 HG21 A:VAL211 4.5 94.0 1.0 HH2 A:TRP234 4.5 80.3 1.0 HD11 A:ILE263 4.6 62.3 1.0 HG11 A:VAL211 4.6 83.7 1.0 CG A:LEU189 4.6 75.5 1.0 HZ3 A:TRP234 4.7 70.8 1.0 CA A:ILE186 4.7 107.5 1.0 HB3 A:LEU189 4.8 89.6 1.0 HD11 A:ILE186 4.8 80.9 1.0 CH2 A:TRP234 4.8 66.2 1.0 HG A:LEU189 4.9 91.5 1.0 CB A:LEU189 4.9 73.9 1.0 CZ3 A:TRP234 4.9 58.2 1.0 HB2 A:TYR258 4.9 75.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.7 occ:1.00 F19 A:U7Q401 0.0 54.7 1.0 C18 A:U7Q401 1.4 45.3 1.0 F21 A:U7Q401 2.2 45.9 1.0 F20 A:U7Q401 2.2 54.1 1.0 C14 A:U7Q401 2.4 49.8 1.0 HB1 A:ALA168 2.9 65.3 1.0 HA A:ALA237 3.0 64.1 1.0 N15 A:U7Q401 3.0 51.7 1.0 HB2 A:ALA168 3.2 65.3 1.0 HD3 A:PRO238 3.2 69.8 1.0 C A:ALA237 3.3 54.0 1.0 C13 A:U7Q401 3.3 50.2 1.0 N A:PRO238 3.3 52.3 1.0 HZ A:PHE221 3.4 66.0 1.0 CB A:ALA168 3.4 53.7 1.0 CA A:ALA237 3.4 52.6 1.0 H131 A:U7Q401 3.5 61.2 1.0 HG3 A:PRO238 3.5 67.9 1.0 HG22 A:ILE236 3.5 63.8 1.0 O A:ILE236 3.5 60.8 1.0 N A:ALA237 3.6 53.5 1.0 CD A:PRO238 3.6 57.4 1.0 C A:ILE236 3.7 54.1 1.0 HA A:PRO238 3.7 66.0 1.0 O A:ALA237 3.8 56.0 1.0 HE1 A:PHE221 3.8 69.2 1.0 O A:HOH505 3.9 52.0 1.0 HB3 A:ALA168 3.9 65.3 1.0 CZ A:PHE221 3.9 54.2 1.0 CG A:PRO238 4.0 55.8 1.0 CA A:PRO238 4.1 54.2 1.0 H A:ALA237 4.1 65.2 1.0 HB A:ILE236 4.1 63.5 1.0 CE1 A:PHE221 4.2 56.9 1.0 C16 A:U7Q401 4.2 50.9 1.0 CG2 A:ILE236 4.2 52.4 1.0 HG21 A:ILE236 4.3 63.8 1.0 C12 A:U7Q401 4.5 49.2 1.0 HD2 A:PRO238 4.5 69.8 1.0 CB A:ILE236 4.5 52.1 1.0 HB2 A:ALA102 4.6 57.9 1.0 HD13 A:ILE149 4.6 59.1 1.0 HA A:ALA168 4.6 62.0 1.0 HD11 A:ILE149 4.6 59.1 1.0 CB A:PRO238 4.7 59.7 1.0 CA A:ALA168 4.7 50.9 1.0 CA A:ILE236 4.7 50.4 1.0 HB1 A:ALA102 4.8 57.9 1.0 H161 A:U7Q401 4.8 62.0 1.0 HG2 A:PRO238 4.9 67.9 1.0 C17 A:U7Q401 4.9 49.7 1.0 HB3 A:PRO238 4.9 72.5 1.0 CB A:ALA237 4.9 61.8 1.0 CE2 A:PHE221 4.9 49.1 1.0 CD1 A:ILE149 5.0 48.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:54.1 occ:1.00 F20 A:U7Q401 0.0 54.1 1.0 C18 A:U7Q401 1.4 45.3 1.0 F21 A:U7Q401 2.2 45.9 1.0 F19 A:U7Q401 2.2 54.7 1.0 C14 A:U7Q401 2.3 49.8 1.0 HZ A:PHE221 2.4 66.0 1.0 HD11 A:ILE149 2.7 59.1 1.0 N15 A:U7Q401 2.8 51.7 1.0 HB2 A:ALA102 3.2 57.9 1.0 HG2 A:PRO129 3.2 57.0 1.0 HD13 A:ILE149 3.2 59.1 1.0 CZ A:PHE221 3.3 54.2 1.0 CD1 A:ILE149 3.4 48.5 1.0 C13 A:U7Q401 3.5 50.2 1.0 HG3 A:PRO238 3.6 67.9 1.0 H131 A:U7Q401 3.7 61.2 1.0 HD12 A:ILE149 3.7 59.1 1.0 O A:HOH505 3.8 52.0 1.0 HB1 A:ALA102 3.9 57.9 1.0 CB A:ALA102 4.0 47.5 1.0 HE1 A:PHE221 4.0 69.2 1.0 HD3 A:PRO238 4.0 69.8 1.0 CG A:PRO129 4.0 46.7 1.0 C16 A:U7Q401 4.1 50.9 1.0 CE1 A:PHE221 4.1 56.9 1.0 HE2 A:PHE221 4.2 59.8 1.0 HD12 A:LEU197 4.2 74.6 1.0 CE2 A:PHE221 4.2 49.1 1.0 HG3 A:PRO129 4.2 57.0 1.0 HB2 A:PRO129 4.4 61.2 1.0 HB3 A:ALA102 4.5 57.9 1.0 HB3 A:PRO129 4.5 61.2 1.0 CG A:PRO238 4.5 55.8 1.0 HD21 A:LEU208 4.5 67.1 1.0 CB A:PRO129 4.5 50.2 1.0 HA A:ALA237 4.6 64.1 1.0 CD A:PRO238 4.6 57.4 1.0 C12 A:U7Q401 4.6 49.2 1.0 H161 A:U7Q401 4.6 62.0 1.0 HB2 A:ALA168 4.6 65.3 1.0 HD22 A:LEU208 4.7 67.1 1.0 CG1 A:ILE149 4.7 39.9 1.0 HG12 A:ILE149 4.7 48.8 1.0 HD11 A:LEU197 4.8 74.6 1.0 O A:ILE236 4.8 60.8 1.0 C17 A:U7Q401 4.9 49.7 1.0 HB1 A:ALA168 4.9 65.3 1.0 HA A:ALA102 4.9 61.0 1.0 N A:PRO238 4.9 52.3 1.0 CD1 A:LEU197 4.9 61.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with A Pyridin Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:45.9 occ:1.00 F21 A:U7Q401 0.0 45.9 1.0 C18 A:U7Q401 1.4 45.3 1.0 F19 A:U7Q401 2.2 54.7 1.0 F20 A:U7Q401 2.2 54.1 1.0 H131 A:U7Q401 2.3 61.2 1.0 C14 A:U7Q401 2.4 49.8 1.0 HD13 A:ILE149 2.6 59.1 1.0 C13 A:U7Q401 2.6 50.2 1.0 HB2 A:ALA168 2.7 65.3 1.0 HD11 A:ILE149 3.2 59.1 1.0 CD1 A:ILE149 3.2 48.5 1.0 HB1 A:ALA102 3.3 57.9 1.0 HD12 A:ILE149 3.4 59.1 1.0 CB A:ALA168 3.5 53.7 1.0 HB1 A:ALA168 3.5 65.3 1.0 HB2 A:ALA102 3.5 57.9 1.0 N15 A:U7Q401 3.6 51.7 1.0 HG3 A:PRO238 3.7 67.9 1.0 HB3 A:ALA168 3.7 65.3 1.0 CB A:ALA102 3.9 47.5 1.0 HA A:PRO238 3.9 66.0 1.0 C12 A:U7Q401 4.0 49.2 1.0 HG21 A:THR265 4.0 66.4 1.0 HG21 A:ILE149 4.2 56.6 1.0 HZ A:PHE221 4.3 66.0 1.0 HB3 A:ALA102 4.4 57.9 1.0 CG A:PRO238 4.5 55.8 1.0 OG1 A:THR265 4.5 57.0 1.0 N A:PRO238 4.5 52.3 1.0 HD3 A:PRO238 4.6 69.8 1.0 HB A:THR265 4.6 67.6 1.0 CA A:PRO238 4.6 54.2 1.0 HB3 A:PRO238 4.6 72.5 1.0 CG1 A:ILE149 4.6 39.9 1.0 C16 A:U7Q401 4.6 50.9 1.0 H111 A:U7Q401 4.7 62.1 1.0 CA A:ALA168 4.8 50.9 1.0 HG23 A:THR166 4.8 73.5 1.0 HG12 A:ILE149 4.8 48.8 1.0 CG2 A:THR265 4.8 54.5 1.0 CD A:PRO238 4.8 57.4 1.0 CB A:PRO238 4.8 59.7 1.0 C A:ALA237 4.9 54.0 1.0 C17 A:U7Q401 4.9 49.7 1.0 HA A:ALA168 4.9 62.0 1.0 N11 A:U7Q401 4.9 50.9 1.0 HA A:ALA102 4.9 61.0 1.0 CB A:THR265 4.9 55.6 1.0 HG22 A:ILE236 4.9 63.8 1.0

C.Schutz, A.Hodzic, M.Hamed, A.S.Abdelsamie, A.M.Kany, M.Bauer, T.Rohrig, S.Schmelz, A.Scrima, W.Blankenfeldt, M.Empting. Divergent Synthesis and Biological Evaluation of 2-(Trifluoromethyl)Pyridines As Virulence-Attenuating Inverse Agonists Targeting Pqsr. Eur.J.Med.Chem. V. 226 13797 2021.
ISSN: ISSN 0223-5234
PubMed: 34520957
DOI: 10.1016/J.EJMECH.2021.113797