Fluorine in PDB 7qa3: Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine

The structure of Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine, PDB code: 7qa3 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)	53.86 / 2.67
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	113.018, 122.61, 112.784, 90, 90, 90
R / Rfree (%)	20.8 / 24.5

The binding sites of Fluorine atom in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine (pdb code 7qa3). 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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine, PDB code: 7qa3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:30.2 occ:1.00 F01 A:A0F401 0.0 30.2 1.0 C02 A:A0F401 1.4 29.3 1.0 F04 A:A0F401 2.2 36.1 1.0 F03 A:A0F401 2.3 28.2 1.0 C05 A:A0F401 2.3 19.3 1.0 HB2 A:ALA102 2.6 42.2 1.0 HD11 A:ILE149 2.7 32.0 1.0 HD13 A:ILE149 2.8 32.0 1.0 HD12 A:ILE149 2.8 32.0 1.0 CD1 A:ILE149 2.9 29.1 1.0 N06 A:A0F401 3.0 21.6 1.0 HB1 A:ALA102 3.1 42.2 1.0 HZ A:PHE221 3.1 35.9 1.0 C30 A:A0F401 3.2 24.9 1.0 CB A:ALA102 3.2 34.4 1.0 H301 A:A0F401 3.3 30.9 1.0 HG2 A:PRO129 3.3 32.9 1.0 HG3 A:PRO238 3.4 45.6 1.0 HB3 A:ALA102 3.7 42.2 1.0 CZ A:PHE221 3.9 29.1 1.0 HD3 A:PRO238 4.2 44.0 1.0 C07 A:A0F401 4.2 31.5 1.0 CG A:PRO129 4.2 26.6 1.0 CG A:PRO238 4.3 37.1 1.0 HG3 A:PRO129 4.4 32.9 1.0 C09 A:A0F401 4.5 32.2 1.0 O A:HOH501 4.5 23.8 1.0 CG1 A:ILE149 4.5 32.1 1.0 HA A:ALA102 4.5 38.7 1.0 HE1 A:PHE221 4.5 35.0 1.0 HB2 A:ALA168 4.5 31.7 1.0 CA A:ALA102 4.5 31.4 1.0 HG21 A:ILE149 4.5 44.2 1.0 CE1 A:PHE221 4.6 28.3 1.0 HE2 A:PHE221 4.7 43.1 1.0 HB1 A:ALA168 4.7 31.7 1.0 CD A:PRO238 4.7 35.9 1.0 HG22 A:ILE236 4.7 43.9 1.0 HG2 A:PRO238 4.7 45.6 1.0 CE2 A:PHE221 4.8 35.1 1.0 HD21 A:LEU207 4.8 67.6 1.0 C08 A:A0F401 4.8 39.8 1.0 HG12 A:ILE149 4.8 39.6 1.0 HG13 A:ILE149 4.8 39.6 1.0 H071 A:A0F401 4.9 38.8 1.0 HD12 A:LEU197 4.9 52.6 1.0 HB2 A:PRO129 4.9 42.3 1.0 HG23 A:ILE149 4.9 44.2 1.0 HA A:PRO238 5.0 39.5 1.0 N A:PRO238 5.0 29.8 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:28.2 occ:1.00 F03 A:A0F401 0.0 28.2 1.0 C02 A:A0F401 1.4 29.3 1.0 F04 A:A0F401 2.2 36.1 1.0 F01 A:A0F401 2.3 30.2 1.0 C05 A:A0F401 2.4 19.3 1.0 N06 A:A0F401 2.8 21.6 1.0 HD3 A:PRO238 2.9 44.0 1.0 HG22 A:ILE236 2.9 43.9 1.0 HA A:ALA237 2.9 41.2 1.0 HG3 A:PRO238 3.3 45.6 1.0 HZ A:PHE221 3.3 35.9 1.0 C A:ALA237 3.4 32.4 1.0 HB1 A:ALA168 3.4 31.7 1.0 HE1 A:PHE221 3.4 35.0 1.0 CA A:ALA237 3.5 33.5 1.0 O A:HOH501 3.5 23.8 1.0 O A:ILE236 3.5 38.0 1.0 CD A:PRO238 3.5 35.9 1.0 N A:PRO238 3.5 29.8 1.0 C30 A:A0F401 3.6 24.9 1.0 N A:ALA237 3.7 29.3 1.0 C A:ILE236 3.7 29.7 1.0 CZ A:PHE221 3.7 29.1 1.0 CE1 A:PHE221 3.8 28.3 1.0 CG2 A:ILE236 3.8 35.8 1.0 H301 A:A0F401 3.8 30.9 1.0 CG A:PRO238 3.9 37.1 1.0 O A:ALA237 3.9 37.9 1.0 HB2 A:ALA168 4.0 31.7 1.0 C07 A:A0F401 4.1 31.5 1.0 HG21 A:ILE236 4.1 43.9 1.0 HA A:PRO238 4.1 39.5 1.0 H A:ALA237 4.2 36.2 1.0 CB A:ALA168 4.2 25.6 1.0 HB2 A:ALA102 4.3 42.2 1.0 HB A:ILE236 4.4 34.7 1.0 CA A:PRO238 4.4 32.1 1.0 HD2 A:PRO238 4.4 44.0 1.0 HG23 A:ILE236 4.4 43.9 1.0 HG2 A:PRO238 4.6 45.6 1.0 HB1 A:ALA102 4.6 42.2 1.0 CB A:ILE236 4.6 28.0 1.0 H071 A:A0F401 4.6 38.8 1.0 HB3 A:ALA168 4.6 31.7 1.0 HE1 A:MET224 4.7 58.1 1.0 C09 A:A0F401 4.8 32.2 1.0 CA A:ILE236 4.8 26.8 1.0 CB A:PRO238 4.8 39.2 1.0 CE2 A:PHE221 4.8 35.1 1.0 HD11 A:ILE149 4.8 32.0 1.0 HD12 A:ILE149 4.8 32.0 1.0 CB A:ALA102 4.9 34.4 1.0 CB A:ALA237 4.9 39.0 1.0 C08 A:A0F401 4.9 39.8 1.0 CD1 A:PHE221 4.9 41.5 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:36.1 occ:1.00 F04 A:A0F401 0.0 36.1 1.0 C02 A:A0F401 1.4 29.3 1.0 F03 A:A0F401 2.2 28.2 1.0 F01 A:A0F401 2.2 30.2 1.0 C05 A:A0F401 2.3 19.3 1.0 HB2 A:ALA168 2.3 31.7 1.0 H301 A:A0F401 2.3 30.9 1.0 HB1 A:ALA168 2.6 31.7 1.0 C30 A:A0F401 2.6 24.9 1.0 CB A:ALA168 2.9 25.6 1.0 HB3 A:ALA168 3.4 31.7 1.0 N06 A:A0F401 3.5 21.6 1.0 HG3 A:PRO238 3.5 45.6 1.0 HA A:PRO238 3.5 39.5 1.0 HB1 A:ALA102 3.6 42.2 1.0 HD12 A:ILE149 3.7 32.0 1.0 HG22 A:ILE236 3.8 43.9 1.0 C09 A:A0F401 4.0 32.2 1.0 HB2 A:ALA102 4.0 42.2 1.0 HG1 A:THR265 4.1 45.3 1.0 HA A:ALA168 4.1 34.4 1.0 CA A:ALA168 4.1 27.8 1.0 N A:PRO238 4.1 29.8 1.0 C A:ALA237 4.1 32.4 1.0 O A:ALA237 4.2 37.9 1.0 CA A:PRO238 4.2 32.1 1.0 HD13 A:ILE149 4.2 32.0 1.0 CG A:PRO238 4.3 37.1 1.0 CB A:ALA102 4.3 34.4 1.0 CD1 A:ILE149 4.3 29.1 1.0 HD3 A:PRO238 4.3 44.0 1.0 HD11 A:ILE149 4.4 32.0 1.0 CD A:PRO238 4.5 35.9 1.0 C07 A:A0F401 4.5 31.5 1.0 HG23 A:THR166 4.6 50.4 1.0 CG2 A:ILE236 4.6 35.8 1.0 HG21 A:ILE236 4.6 43.9 1.0 HB3 A:PRO238 4.6 48.0 1.0 CB A:PRO238 4.7 39.2 1.0 HA A:ALA237 4.7 41.2 1.0 HG21 A:THR265 4.7 51.8 1.0 N A:ALA168 4.8 35.9 1.0 HZ A:PHE221 4.8 35.9 1.0 H101 A:A0F401 4.8 39.6 1.0 C08 A:A0F401 4.8 39.8 1.0 HB3 A:ALA102 4.8 42.2 1.0 HG21 A:ILE149 4.8 44.2 1.0 HG23 A:ILE236 4.9 43.9 1.0 CA A:ALA237 4.9 33.5 1.0 OG1 A:THR265 4.9 36.9 1.0 N10 A:A0F401 4.9 32.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:41.5 occ:1.00 F01 B:A0F401 0.0 41.5 1.0 C02 B:A0F401 1.4 39.8 1.0 F04 B:A0F401 2.2 37.5 1.0 C05 B:A0F401 2.3 35.0 1.0 F03 B:A0F401 2.3 44.7 1.0 HD11 B:ILE149 2.4 45.9 1.0 HD13 B:ILE149 2.6 45.9 1.0 CD1 B:ILE149 2.8 37.4 1.0 HB2 B:ALA102 2.9 48.0 1.0 HD12 B:ILE149 2.9 45.9 1.0 N06 B:A0F401 3.0 36.0 1.0 HZ B:PHE221 3.1 50.2 1.0 C30 B:A0F401 3.1 35.8 1.0 HG2 B:PRO129 3.2 41.8 1.0 H301 B:A0F401 3.2 43.9 1.0 HB1 B:ALA102 3.3 48.0 1.0 CB B:ALA102 3.5 39.2 1.0 HG3 B:PRO238 3.8 55.8 1.0 CZ B:PHE221 3.9 41.0 1.0 HB3 B:ALA102 4.0 48.0 1.0 CG B:PRO129 4.1 34.0 1.0 C07 B:A0F401 4.1 33.2 1.0 HD3 B:PRO238 4.3 56.3 1.0 C09 B:A0F401 4.3 35.3 1.0 HG3 B:PRO129 4.3 41.8 1.0 CG1 B:ILE149 4.3 44.3 1.0 HG22 B:ILE236 4.4 53.8 1.0 HD21 B:LEU208 4.5 65.8 1.0 HE2 B:PHE221 4.5 62.7 1.0 HG12 B:ILE149 4.5 54.2 1.0 HB2 B:ALA168 4.6 55.4 1.0 HE1 B:PHE221 4.6 50.2 1.0 HB2 B:PRO129 4.6 41.0 1.0 CG B:PRO238 4.6 45.7 1.0 HB3 B:PRO129 4.7 41.0 1.0 CE2 B:PHE221 4.7 51.4 1.0 C08 B:A0F401 4.7 32.4 1.0 HG13 B:ILE149 4.7 54.2 1.0 CB B:PRO129 4.7 33.4 1.0 CE1 B:PHE221 4.7 41.0 1.0 HA B:ALA102 4.7 54.9 1.0 HD21 B:LEU207 4.8 60.3 1.0 CA B:ALA102 4.8 44.9 1.0 H071 B:A0F401 4.8 40.9 1.0 HD11 B:LEU207 4.8 66.4 1.0 HG21 B:ILE149 4.8 46.9 1.0 HD12 B:LEU197 4.8 60.1 1.0 HB1 B:ALA168 4.9 55.4 1.0 CD B:PRO238 4.9 46.0 1.0 HA B:ALA237 4.9 54.8 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:44.7 occ:1.00 F03 B:A0F401 0.0 44.7 1.0 C02 B:A0F401 1.4 39.8 1.0 F04 B:A0F401 2.2 37.5 1.0 F01 B:A0F401 2.3 41.5 1.0 C05 B:A0F401 2.4 35.0 1.0 HG22 B:ILE236 2.7 53.8 1.0 N06 B:A0F401 2.7 36.0 1.0 HA B:ALA237 2.8 54.8 1.0 HD3 B:PRO238 3.1 56.3 1.0 O B:ILE236 3.1 49.1 1.0 HZ B:PHE221 3.2 50.2 1.0 HE1 B:PHE221 3.4 50.2 1.0 CA B:ALA237 3.5 44.8 1.0 C30 B:A0F401 3.5 35.8 1.0 C B:ILE236 3.5 39.7 1.0 HB1 B:ALA168 3.6 55.4 1.0 C B:ALA237 3.6 45.9 1.0 CG2 B:ILE236 3.6 44.0 1.0 CZ B:PHE221 3.7 41.0 1.0 N B:ALA237 3.7 44.5 1.0 HG3 B:PRO238 3.8 55.8 1.0 CD B:PRO238 3.8 46.0 1.0 H301 B:A0F401 3.8 43.9 1.0 CE1 B:PHE221 3.8 41.0 1.0 N B:PRO238 3.8 43.8 1.0 HG23 B:ILE236 3.9 53.8 1.0 C07 B:A0F401 4.0 33.2 1.0 HB2 B:ALA168 4.1 55.4 1.0 O B:ALA237 4.1 44.0 1.0 HG21 B:ILE236 4.1 53.8 1.0 H B:ALA237 4.3 54.5 1.0 HB B:ILE236 4.3 44.4 1.0 CB B:ALA168 4.3 45.3 1.0 CG B:PRO238 4.3 45.7 1.0 CB B:ILE236 4.4 36.1 1.0 H071 B:A0F401 4.5 40.9 1.0 HA B:PRO238 4.5 58.7 1.0 HD2 B:PRO238 4.6 56.3 1.0 HB2 B:ALA102 4.6 48.0 1.0 CA B:ILE236 4.6 35.5 1.0 HD11 B:ILE149 4.7 45.9 1.0 HB3 B:ALA168 4.7 55.4 1.0 C09 B:A0F401 4.7 35.3 1.0 CE2 B:PHE221 4.7 51.4 1.0 HD12 B:LEU197 4.7 60.1 1.0 CA B:PRO238 4.7 48.1 1.0 C08 B:A0F401 4.8 32.4 1.0 HB1 B:ALA102 4.8 48.0 1.0 CB B:ALA237 4.9 59.3 1.0 HD13 B:ILE149 4.9 45.9 1.0 HG2 B:PRO129 4.9 41.8 1.0 HE2 B:PHE221 5.0 62.7 1.0 HE1 B:MET224 5.0 72.5 1.0 HD12 B:ILE149 5.0 45.9 1.0 CD1 B:PHE221 5.0 56.3 1.0 HE3 B:MET224 5.0 72.5 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine


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 Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Phenoxyphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:37.5 occ:1.00 F04 B:A0F401 0.0 37.5 1.0 C02 B:A0F401 1.3 39.8 1.0 F01 B:A0F401 2.2 41.5 1.0 H301 B:A0F401 2.2 43.9 1.0 F03 B:A0F401 2.2 44.7 1.0 C05 B:A0F401 2.3 35.0 1.0 HB2 B:ALA168 2.4 55.4 1.0 C30 B:A0F401 2.5 35.8 1.0 HB1 B:ALA168 2.8 55.4 1.0 CB B:ALA168 3.0 45.3 1.0 HB3 B:ALA168 3.4 55.4 1.0 N06 B:A0F401 3.4 36.0 1.0 HA B:PRO238 3.7 58.7 1.0 HG22 B:ILE236 3.7 53.8 1.0 HB1 B:ALA102 3.7 48.0 1.0 HG3 B:PRO238 3.7 55.8 1.0 HD12 B:ILE149 3.7 45.9 1.0 HD13 B:ILE149 3.8 45.9 1.0 C09 B:A0F401 3.9 35.3 1.0 CD1 B:ILE149 4.1 37.4 1.0 C B:ALA237 4.1 45.9 1.0 O B:ALA237 4.1 44.0 1.0 N B:PRO238 4.1 43.8 1.0 HD11 B:ILE149 4.1 45.9 1.0 HG1 B:THR265 4.1 46.0 1.0 HB2 B:ALA102 4.1 48.0 1.0 HD3 B:PRO238 4.2 56.3 1.0 CA B:ALA168 4.2 34.0 1.0 HA B:ALA168 4.3 41.9 1.0 CA B:PRO238 4.3 48.1 1.0 CB B:ALA102 4.4 39.2 1.0 HA B:ALA237 4.4 54.8 1.0 CG B:PRO238 4.4 45.7 1.0 CG2 B:ILE236 4.4 44.0 1.0 HG23 B:ILE236 4.4 53.8 1.0 C07 B:A0F401 4.5 33.2 1.0 CD B:PRO238 4.5 46.0 1.0 HZ B:PHE221 4.5 50.2 1.0 HG21 B:THR265 4.6 63.2 1.0 HB3 B:PRO238 4.6 65.1 1.0 HG21 B:ILE236 4.7 53.8 1.0 C08 B:A0F401 4.7 32.4 1.0 H101 B:A0F401 4.7 44.6 1.0 CA B:ALA237 4.7 44.8 1.0 CB B:PRO238 4.8 53.4 1.0 N10 B:A0F401 4.8 36.3 1.0 HB3 B:ALA102 4.9 48.0 1.0 N B:ALA168 4.9 31.3 1.0 N B:ALA237 4.9 44.5 1.0 OG1 B:THR265 5.0 37.5 1.0

W.Blankenfeldt, S.Schmelz. Divergent Synthesis and Biological Evaluation of Inverse Agonists Targeting Pqsr To Be Published.