Fluorine in PDB 7qav: Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine, PDB code: 7qav 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)	53.29 / 2.65
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	108.728, 121.152, 112.113, 90, 90, 90
R / Rfree (%)	24.8 / 28.7

The binding sites of Fluorine atom in the Crystal Structure of Pqsr (Mvfr) Ligand-Binding Domain in Complex with Compound N-((2-(4-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine (pdb code 7qav). 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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine, PDB code: 7qav:
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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:43.6 occ:1.00 F A:XBH401 0.0 43.6 1.0 C A:XBH401 1.3 36.8 1.0 F2 A:XBH401 2.1 33.6 1.0 F1 A:XBH401 2.1 42.4 1.0 C1 A:XBH401 2.4 30.4 1.0 HB1 A:ALA168 2.7 49.8 1.0 HB2 A:ALA168 2.7 49.8 1.0 N A:XBH401 3.1 30.8 1.0 CB A:ALA168 3.1 39.7 1.0 HG3 A:PRO238 3.2 43.4 1.0 C18 A:XBH401 3.3 40.3 1.0 HA A:PRO238 3.3 43.9 1.0 H15 A:XBH401 3.4 50.5 1.0 HG22 A:ILE236 3.4 57.0 1.0 C A:ALA237 3.4 36.9 1.0 N A:PRO238 3.5 32.8 1.0 O A:ALA237 3.6 35.0 1.0 HB3 A:ALA168 3.7 49.8 1.0 CA A:PRO238 3.8 34.8 1.0 HA A:ALA237 3.8 45.4 1.0 CG A:PRO238 3.9 34.4 1.0 HD3 A:PRO238 3.9 51.9 1.0 CD A:PRO238 4.0 41.5 1.0 CA A:ALA237 4.0 36.0 1.0 HA A:ALA168 4.1 57.2 1.0 HZ A:PHE221 4.2 58.2 1.0 HB3 A:PRO238 4.2 45.3 1.0 O A:ILE236 4.2 36.1 1.0 HB1 A:ALA102 4.2 46.5 1.0 N A:ALA237 4.2 28.2 1.0 CA A:ALA168 4.2 45.9 1.0 CB A:PRO238 4.2 36.0 1.0 C2 A:XBH401 4.3 36.5 1.0 HB2 A:ALA102 4.3 46.5 1.0 C A:ILE236 4.3 33.1 1.0 CG2 A:ILE236 4.3 45.7 1.0 C4 A:XBH401 4.5 41.6 1.0 HE1 A:PHE221 4.5 51.9 1.0 HD12 A:ILE149 4.6 44.6 1.0 H A:ALA237 4.6 36.0 1.0 HG21 A:ILE236 4.7 57.0 1.0 CZ A:PHE221 4.7 46.7 1.0 CB A:ALA102 4.7 37.0 1.0 H A:PHE169 4.7 57.8 1.0 HG2 A:PRO238 4.8 43.4 1.0 HD11 A:ILE149 4.8 44.6 1.0 HG23 A:ILE236 4.8 57.0 1.0 HB A:ILE236 4.9 57.5 1.0 C3 A:XBH401 4.9 41.0 1.0 CE1 A:PHE221 4.9 41.5 1.0 HD13 A:ILE149 4.9 44.6 1.0 CD1 A:ILE149 5.0 35.4 1.0 HD2 A:PRO238 5.0 51.9 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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:42.4 occ:1.00 F1 A:XBH401 0.0 42.4 1.0 C A:XBH401 1.3 36.8 1.0 F2 A:XBH401 2.1 33.6 1.0 F A:XBH401 2.1 43.6 1.0 C1 A:XBH401 2.4 30.4 1.0 H15 A:XBH401 2.5 50.5 1.0 C18 A:XBH401 2.8 40.3 1.0 HB2 A:ALA168 2.8 49.8 1.0 HD12 A:ILE149 2.8 44.6 1.0 HB1 A:ALA102 3.1 46.5 1.0 HD13 A:ILE149 3.2 44.6 1.0 CD1 A:ILE149 3.3 35.4 1.0 HD11 A:ILE149 3.5 44.6 1.0 N A:XBH401 3.5 30.8 1.0 CB A:ALA168 3.6 39.7 1.0 HB2 A:ALA102 3.7 46.5 1.0 HB1 A:ALA168 3.7 49.8 1.0 CB A:ALA102 3.8 37.0 1.0 HG1 A:THR265 3.9 52.9 1.0 HB3 A:ALA168 3.9 49.8 1.0 HG3 A:PRO238 4.0 43.4 1.0 HG23 A:THR166 4.0 41.2 1.0 HG21 A:ILE149 4.0 34.4 1.0 C4 A:XBH401 4.1 41.6 1.0 HB A:THR265 4.2 47.5 1.0 HA A:PRO238 4.2 43.9 1.0 HG21 A:THR265 4.2 57.9 1.0 HB3 A:ALA102 4.2 46.5 1.0 HB3 A:PRO238 4.4 45.3 1.0 HG21 A:THR166 4.4 41.2 1.0 OG1 A:THR265 4.6 42.3 1.0 C2 A:XBH401 4.6 36.5 1.0 CG2 A:THR166 4.6 32.6 1.0 CB A:THR265 4.7 37.8 1.0 CG1 A:ILE149 4.7 33.0 1.0 CA A:ALA168 4.8 45.9 1.0 CG A:PRO238 4.8 34.4 1.0 HA A:ALA168 4.8 57.2 1.0 CA A:PRO238 4.9 34.8 1.0 HG22 A:THR166 4.9 41.2 1.0 H2 A:XBH401 4.9 48.2 1.0 CG2 A:ILE149 4.9 26.9 1.0 CB A:PRO238 4.9 36.0 1.0 C3 A:XBH401 4.9 41.0 1.0 CG2 A:THR265 4.9 46.5 1.0 HG22 A:ILE236 4.9 57.0 1.0 HA A:ALA102 5.0 38.2 1.0 O A:LYS167 5.0 43.8 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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:33.6 occ:1.00 F2 A:XBH401 0.0 33.6 1.0 C A:XBH401 1.3 36.8 1.0 F A:XBH401 2.1 43.6 1.0 F1 A:XBH401 2.1 42.4 1.0 C1 A:XBH401 2.4 30.4 1.0 HB2 A:ALA102 2.6 46.5 1.0 N A:XBH401 2.7 30.8 1.0 HD11 A:ILE149 2.9 44.6 1.0 HZ A:PHE221 2.9 58.2 1.0 HB1 A:ALA102 3.0 46.5 1.0 HG3 A:PRO238 3.0 43.4 1.0 CB A:ALA102 3.2 37.0 1.0 HD12 A:ILE149 3.3 44.6 1.0 HD13 A:ILE149 3.3 44.6 1.0 CD1 A:ILE149 3.3 35.4 1.0 C18 A:XBH401 3.6 40.3 1.0 CZ A:PHE221 3.7 46.7 1.0 HB3 A:ALA102 3.8 46.5 1.0 H15 A:XBH401 3.9 50.5 1.0 C2 A:XBH401 4.0 36.5 1.0 CG A:PRO238 4.0 34.4 1.0 HA A:ALA102 4.2 38.2 1.0 HD3 A:PRO238 4.3 51.9 1.0 HE1 A:PHE221 4.3 51.9 1.0 HG2 A:PRO129 4.3 39.3 1.0 HB2 A:ALA168 4.3 49.8 1.0 CA A:ALA102 4.4 30.9 1.0 CE1 A:PHE221 4.5 41.5 1.0 HE2 A:PHE221 4.5 59.6 1.0 HG2 A:PRO238 4.5 43.4 1.0 CE2 A:PHE221 4.6 47.9 1.0 HB3 A:PRO238 4.6 45.3 1.0 H A:XBH401 4.6 46.0 1.0 CD A:PRO238 4.6 41.5 1.0 HA A:PRO238 4.7 43.9 1.0 N A:PRO238 4.7 32.8 1.0 C4 A:XBH401 4.7 41.6 1.0 HB1 A:ALA168 4.7 49.8 1.0 CB A:PRO238 4.8 36.0 1.0 CG1 A:ILE149 4.8 33.0 1.0 HA A:ALA237 4.8 45.4 1.0 C3 A:XBH401 4.9 41.0 1.0 HG21 A:ILE149 4.9 34.4 1.0 HG3 A:PRO129 5.0 39.3 1.0 HG22 A:ILE236 5.0 57.0 1.0 CA A:PRO238 5.0 34.8 1.0 CB A:ALA168 5.0 39.7 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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:45.8 occ:1.00 F B:XBH401 0.0 45.8 1.0 C B:XBH401 1.3 36.0 1.0 F1 B:XBH401 2.1 29.5 1.0 F2 B:XBH401 2.1 32.7 1.0 C1 B:XBH401 2.4 38.6 1.0 H15 B:XBH401 2.4 63.0 1.0 HB2 B:ALA168 2.6 36.5 1.0 C18 B:XBH401 2.7 50.7 1.0 HB1 B:ALA102 3.4 53.9 1.0 HD13 B:ILE149 3.4 52.5 1.0 CB B:ALA168 3.4 32.0 1.0 HB1 B:ALA168 3.5 36.5 1.0 N B:XBH401 3.5 32.6 1.0 HG21 B:THR265 3.6 62.4 1.0 HG3 B:PRO238 3.6 49.6 1.0 HG1 B:THR265 3.7 73.5 1.0 HB2 B:ALA102 3.8 53.9 1.0 HD12 B:ILE149 3.8 52.5 1.0 HB3 B:ALA168 3.9 36.5 1.0 HA B:PRO238 3.9 41.9 1.0 CD1 B:ILE149 3.9 41.9 1.0 HD11 B:ILE149 4.0 52.5 1.0 HG23 B:THR265 4.0 62.4 1.0 CB B:ALA102 4.0 43.1 1.0 OG1 B:THR265 4.1 59.5 1.0 C4 B:XBH401 4.1 43.1 1.0 HG23 B:THR166 4.2 54.1 1.0 CG2 B:THR265 4.2 50.2 1.0 HB3 B:ALA102 4.4 53.9 1.0 HG22 B:ILE236 4.5 51.8 1.0 CG B:PRO238 4.5 39.5 1.0 HG21 B:THR166 4.5 54.1 1.0 HA B:ALA168 4.6 47.4 1.0 HB3 B:PRO238 4.6 46.7 1.0 CA B:ALA168 4.6 37.8 1.0 CA B:PRO238 4.6 33.1 1.0 C2 B:XBH401 4.6 35.5 1.0 HG23 B:ILE236 4.7 51.8 1.0 HG21 B:ILE149 4.7 39.4 1.0 N B:PRO238 4.7 33.1 1.0 O B:LYS167 4.7 56.1 1.0 CG2 B:THR166 4.8 43.3 1.0 O B:ALA237 4.8 42.9 1.0 HD3 B:PRO238 4.8 49.0 1.0 CB B:PRO238 4.8 37.1 1.0 CB B:THR265 4.8 52.1 1.0 HZ B:PHE221 4.9 52.9 1.0 HG21 B:ILE236 4.9 51.8 1.0 H2 B:XBH401 4.9 43.8 1.0 CG2 B:ILE236 4.9 41.4 1.0 C B:ALA237 4.9 37.4 1.0 C3 B:XBH401 4.9 41.9 1.0 CD B:PRO238 5.0 39.0 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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:29.5 occ:1.00 F1 B:XBH401 0.0 29.5 1.0 C B:XBH401 1.3 36.0 1.0 F2 B:XBH401 2.1 32.7 1.0 F B:XBH401 2.1 45.8 1.0 C1 B:XBH401 2.4 38.6 1.0 HB2 B:ALA102 2.6 53.9 1.0 N B:XBH401 2.8 32.6 1.0 HD11 B:ILE149 2.8 52.5 1.0 HZ B:PHE221 3.0 52.9 1.0 HD13 B:ILE149 3.0 52.5 1.0 HB1 B:ALA102 3.1 53.9 1.0 CB B:ALA102 3.3 43.1 1.0 HG3 B:PRO238 3.3 49.6 1.0 CD1 B:ILE149 3.3 41.9 1.0 C18 B:XBH401 3.5 50.7 1.0 HD12 B:ILE149 3.6 52.5 1.0 HB3 B:ALA102 3.7 53.9 1.0 HG2 B:PRO129 3.8 49.1 1.0 H15 B:XBH401 3.8 63.0 1.0 CZ B:PHE221 3.8 42.3 1.0 C2 B:XBH401 4.1 35.5 1.0 HG3 B:PRO129 4.1 49.1 1.0 HD3 B:PRO238 4.2 49.0 1.0 CG B:PRO238 4.2 39.5 1.0 HG22 B:ILE236 4.4 51.8 1.0 CG B:PRO129 4.4 39.1 1.0 HE1 B:PHE221 4.4 46.5 1.0 HA B:ALA102 4.5 53.1 1.0 HD11 B:LEU208 4.5 87.1 1.0 CA B:ALA102 4.5 42.5 1.0 CE1 B:PHE221 4.6 36.9 1.0 HB2 B:ALA168 4.6 36.5 1.0 CD B:PRO238 4.6 39.0 1.0 HG2 B:PRO238 4.6 49.6 1.0 HE2 B:PHE221 4.6 67.2 1.0 C4 B:XBH401 4.7 43.1 1.0 H B:XBH401 4.7 44.7 1.0 CG1 B:ILE149 4.7 40.4 1.0 CE2 B:PHE221 4.7 54.2 1.0 HG12 B:ILE149 4.8 50.6 1.0 HG21 B:ILE149 4.8 39.4 1.0 C3 B:XBH401 4.9 41.9 1.0 HA B:PRO238 4.9 41.9 1.0 HB1 B:ALA168 5.0 36.5 1.0 N B:PRO238 5.0 33.1 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-Cyclopropylphenyl)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-Cyclopropylphenyl)Thiazol-5-Yl)Methyl)-2- (Trifluoromethyl)Pyridin-4-Amine within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:32.7 occ:1.00 F2 B:XBH401 0.0 32.7 1.0 C B:XBH401 1.3 36.0 1.0 F1 B:XBH401 2.1 29.5 1.0 F B:XBH401 2.1 45.8 1.0 C1 B:XBH401 2.4 38.6 1.0 N B:XBH401 3.0 32.6 1.0 HG3 B:PRO238 3.0 49.6 1.0 HG22 B:ILE236 3.0 51.8 1.0 HD3 B:PRO238 3.1 49.0 1.0 HB1 B:ALA168 3.2 36.5 1.0 C18 B:XBH401 3.4 50.7 1.0 HB2 B:ALA168 3.4 36.5 1.0 C B:ALA237 3.4 37.4 1.0 N B:PRO238 3.4 33.1 1.0 HG23 B:ILE236 3.4 51.8 1.0 HA B:ALA237 3.5 40.1 1.0 H15 B:XBH401 3.6 63.0 1.0 HA B:PRO238 3.6 41.9 1.0 HZ B:PHE221 3.6 52.9 1.0 CD B:PRO238 3.6 39.0 1.0 O B:ALA237 3.6 42.9 1.0 CG2 B:ILE236 3.6 41.4 1.0 CG B:PRO238 3.7 39.5 1.0 CB B:ALA168 3.8 32.0 1.0 HE1 B:PHE221 3.8 46.5 1.0 CA B:ALA237 3.8 31.6 1.0 O B:ILE236 3.9 39.0 1.0 CA B:PRO238 3.9 33.1 1.0 HG21 B:ILE236 4.0 51.8 1.0 N B:ALA237 4.1 28.6 1.0 HB2 B:ALA102 4.1 53.9 1.0 C B:ILE236 4.1 33.1 1.0 CZ B:PHE221 4.1 42.3 1.0 C2 B:XBH401 4.2 35.5 1.0 HB1 B:ALA102 4.3 53.9 1.0 CE1 B:PHE221 4.3 36.9 1.0 HB3 B:ALA168 4.4 36.5 1.0 CB B:PRO238 4.4 37.1 1.0 HG2 B:PRO238 4.5 49.6 1.0 HD2 B:PRO238 4.5 49.0 1.0 C4 B:XBH401 4.5 43.1 1.0 H B:ALA237 4.5 36.4 1.0 HA B:ALA168 4.6 47.4 1.0 HB3 B:PRO238 4.6 46.7 1.0 CB B:ALA102 4.7 43.1 1.0 CA B:ALA168 4.8 37.8 1.0 HD11 B:ILE149 4.8 52.5 1.0 HD13 B:ILE149 4.8 52.5 1.0 H B:XBH401 4.9 44.7 1.0 C3 B:XBH401 4.9 41.9 1.0 CB B:ILE236 4.9 34.4 1.0

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