Fluorine in PDB 7rkr: Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate

The structure of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate, PDB code: 7rkr was solved by V.Sharma, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	70.38 / 1.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.86, 55.35, 71.49, 90, 100.12, 90
R / Rfree (%)	18.8 / 23.9

The structure of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Iron	(Fe)	1 atom

The binding sites of Fluorine atom in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate (pdb code 7rkr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate, PDB code: 7rkr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:40.9 occ:1.00 F3 A:L49502 0.0 40.9 1.0 C15 A:L49502 1.3 41.6 1.0 F1 A:L49502 2.1 46.0 1.0 F2 A:L49502 2.1 45.7 1.0 C14 A:L49502 2.3 32.6 1.0 C13 A:L49502 2.7 28.1 1.0 N A:GLY290 3.0 36.4 1.0 C A:ALA289 3.1 35.6 1.0 O A:ALA289 3.2 34.9 1.0 CA A:GLY290 3.2 38.1 1.0 CB A:ALA289 3.5 31.6 1.0 C16 A:L49502 3.5 32.8 1.0 CA A:ALA289 3.9 31.3 1.0 CG2 A:VAL135 4.0 36.5 1.0 C A:L49502 4.1 33.9 1.0 O A:ILE286 4.1 33.1 1.0 C A:GLY290 4.5 37.8 1.0 CB A:ALA293 4.6 34.5 1.0 CG1 A:VAL135 4.6 36.3 1.0 CB A:VAL135 4.7 35.0 1.0 C17 A:L49502 4.7 31.7 1.0 O A:GLY290 4.8 33.1 1.0 C18 A:L49502 4.9 32.2 1.0 N A:ALA289 4.9 33.9 1.0 CMD A:HEM501 5.0 34.2 1.0 O A:L49502 5.0 36.3 1.0

Fluorine binding site 2 out of 4 in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:46.0 occ:1.00 F1 A:L49502 0.0 46.0 1.0 C15 A:L49502 1.3 41.6 1.0 F3 A:L49502 2.1 40.9 1.0 F2 A:L49502 2.1 45.7 1.0 C14 A:L49502 2.3 32.6 1.0 C16 A:L49502 2.9 32.8 1.0 C13 A:L49502 3.4 28.1 1.0 CG2 A:VAL119 3.5 52.4 1.0 CB A:ALA289 3.5 31.6 1.0 CG2 A:VAL135 4.2 36.5 1.0 C17 A:L49502 4.2 31.7 1.0 O A:ILE286 4.2 33.1 1.0 N A:GLY290 4.4 36.4 1.0 C A:ALA289 4.4 35.6 1.0 C A:L49502 4.6 33.9 1.0 CG1 A:VAL119 4.6 51.6 1.0 CA A:ALA289 4.6 31.3 1.0 CG2 A:ILE286 4.6 40.3 1.0 CB A:VAL119 4.7 47.5 1.0 CA A:ILE286 4.8 36.3 1.0 O A:ALA289 4.8 34.9 1.0 C18 A:L49502 4.9 32.2 1.0 CG2 A:VAL132 4.9 38.4 1.0 C A:ILE286 4.9 32.9 1.0 CA A:GLY290 5.0 38.1 1.0

Fluorine binding site 3 out of 4 in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:45.7 occ:1.00 F2 A:L49502 0.0 45.7 1.0 C15 A:L49502 1.3 41.6 1.0 F1 A:L49502 2.1 46.0 1.0 F3 A:L49502 2.1 40.9 1.0 C14 A:L49502 2.3 32.6 1.0 C16 A:L49502 2.8 32.8 1.0 C13 A:L49502 3.4 28.1 1.0 CG2 A:VAL135 3.6 36.5 1.0 CMD A:HEM501 3.6 34.2 1.0 CB A:VAL135 3.9 35.0 1.0 CG2 A:VAL132 4.1 38.4 1.0 C17 A:L49502 4.2 31.7 1.0 CA A:VAL132 4.2 39.0 1.0 CG1 A:VAL135 4.2 36.3 1.0 C A:L49502 4.6 33.9 1.0 CB A:VAL132 4.6 38.0 1.0 O A:VAL132 4.8 37.6 1.0 C18 A:L49502 4.8 32.2 1.0 CG1 A:VAL132 4.9 42.8 1.0 C2D A:HEM501 4.9 33.7 1.0 N A:VAL132 5.0 35.5 1.0

Fluorine binding site 4 out of 4 in the Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Naegleria Fowleri CYP51 (NFCYP51) Complex with (S)-1-(4-Fluorophenyl)- 2-(1H-Imidazol-1-Yl)Ethyl 3-(Trifluoromethyl)Benzoate within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:45.3 occ:1.00 F A:L49502 0.0 45.3 1.0 C6 A:L49502 1.3 42.4 1.0 C5 A:L49502 2.3 42.1 1.0 C7 A:L49502 2.4 40.1 1.0 CZ A:PHE109 3.2 37.6 1.0 CE1 A:PHE109 3.3 38.4 1.0 CG A:MET110 3.4 34.7 1.0 CD1 A:TYR107 3.6 40.2 1.0 C4 A:L49502 3.6 40.1 1.0 C8 A:L49502 3.6 42.3 1.0 CG A:TYR107 3.9 39.6 1.0 CB A:TYR107 3.9 38.9 1.0 SD A:MET110 4.0 40.5 1.0 O A:HOH691 4.0 54.7 1.0 C3 A:L49502 4.1 38.4 1.0 CE1 A:TYR107 4.2 46.9 1.0 CE2 A:PHE109 4.3 36.9 1.0 CA A:TYR107 4.3 36.6 1.0 CD1 A:PHE109 4.4 38.8 1.0 O A:TYR107 4.4 36.4 1.0 CD2 A:TYR107 4.7 41.3 1.0 CB A:MET110 4.7 32.9 1.0 O A:HOH699 4.8 62.6 1.0 CD2 A:LEU467 4.9 57.4 1.0 C A:TYR107 4.9 37.8 1.0 CZ A:TYR107 5.0 46.4 1.0

V.Sharma, L.M.Podust. Structure Aided Approaches to Develop Naegleria Fowleri Specific Brain Permeable CYP51 Inhibitors. To Be Published.