Fluorine in PDB 6ay6: Naegleria Fowleri CYP51-Voriconazole Complex

The structure of Naegleria Fowleri CYP51-Voriconazole Complex, PDB code: 6ay6 was solved by A.Debnath, C.M.Calvet, G.Jennings, W.Zhou, A.Aksenov, M.Luth, R.Abagyan, W.D.Nes, J.H.Mckerrow, L.M.Podust, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	71.92 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.180, 55.340, 73.220, 90.00, 100.80, 90.00
R / Rfree (%)	21.9 / 29

The structure of Naegleria Fowleri CYP51-Voriconazole Complex also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Fluorine atom in the Naegleria Fowleri CYP51-Voriconazole Complex (pdb code 6ay6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Naegleria Fowleri CYP51-Voriconazole Complex, PDB code: 6ay6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


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-Voriconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:76.7 occ:1.00 F1 A:VOR501 0.0 76.7 1.0 C16 A:VOR501 1.3 66.5 1.0 C19 A:VOR501 2.4 66.5 1.0 C13 A:VOR501 2.4 61.1 1.0 C10 A:VOR501 2.8 64.6 1.0 C12 A:VOR501 2.9 66.0 1.0 C11 A:VOR501 2.9 69.2 1.0 CD1 A:PHE292 3.0 66.0 1.0 CE1 A:PHE292 3.3 65.5 1.0 C22 A:VOR501 3.6 71.6 1.0 C17 A:VOR501 3.6 60.3 1.0 N5 A:VOR501 3.7 66.6 1.0 C14 A:VOR501 3.8 65.6 1.0 CZ A:PHE114 3.8 68.6 1.0 N7 A:VOR501 3.9 72.1 1.0 F2 A:VOR501 4.1 80.1 1.0 C20 A:VOR501 4.1 60.5 1.0 N A:ALA293 4.1 66.8 1.0 C15 A:VOR501 4.1 69.4 1.0 CG A:PHE292 4.2 63.9 1.0 O4 A:VOR501 4.2 70.2 1.0 CE A:MET110 4.3 94.8 1.0 CA A:ALA293 4.4 61.5 1.0 CZ A:PHE292 4.6 66.3 1.0 C18 A:VOR501 4.6 73.5 1.0 CE2 A:PHE114 4.6 68.1 1.0 CB A:PHE292 4.7 62.5 1.0 CE1 A:PHE114 4.7 70.3 1.0 F3 A:VOR501 4.7 76.3 1.0 CB A:ALA293 4.7 58.4 1.0 C A:PHE292 4.8 64.0 1.0 C21 A:VOR501 4.9 72.0 1.0

Fluorine binding site 2 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


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-Voriconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:80.1 occ:1.00 F2 A:VOR501 0.0 80.1 1.0 C18 A:VOR501 1.3 73.5 1.0 C23 A:VOR501 2.4 76.5 1.0 C15 A:VOR501 2.4 69.4 1.0 C11 A:VOR501 2.9 69.2 1.0 N9 A:VOR501 3.6 65.1 1.0 N6 A:VOR501 3.6 75.5 1.0 CG A:LEU467 3.8 90.1 1.0 C12 A:VOR501 3.9 66.0 1.0 C14 A:VOR501 4.0 65.6 1.0 C10 A:VOR501 4.0 64.6 1.0 F1 A:VOR501 4.1 76.7 1.0 C24 A:VOR501 4.1 70.7 1.0 CD2 A:LEU358 4.1 65.2 1.0 CD2 A:LEU467 4.1 91.6 1.0 CE1 A:PHE292 4.2 65.5 1.0 CB A:LEU467 4.4 88.6 1.0 CE A:MET110 4.6 94.8 1.0 CG2 A:VAL468 4.7 72.9 1.0 O A:LEU467 4.7 87.5 1.0 CZ A:PHE292 4.8 66.3 1.0 C A:LEU467 4.8 82.2 1.0 O4 A:VOR501 4.9 70.2 1.0 SD A:MET110 4.9 97.0 1.0 CD1 A:LEU467 4.9 83.4 1.0 C16 A:VOR501 5.0 66.5 1.0

Fluorine binding site 3 out of 3 in the Naegleria Fowleri CYP51-Voriconazole Complex


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-Voriconazole Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F501 b:76.3 occ:1.00 F3 A:VOR501 0.0 76.3 1.0 C22 A:VOR501 1.3 71.6 1.0 C20 A:VOR501 2.4 60.5 1.0 C19 A:VOR501 2.4 66.5 1.0 O A:ALA289 3.2 65.2 1.0 CB A:ALA289 3.5 59.9 1.0 C16 A:VOR501 3.6 66.5 1.0 C A:ALA289 3.6 63.1 1.0 C17 A:VOR501 3.6 60.3 1.0 CA A:ALA289 4.1 63.4 1.0 C13 A:VOR501 4.1 61.1 1.0 CMD A:HEM502 4.2 56.6 1.0 CB A:ALA293 4.3 58.4 1.0 N A:GLY290 4.4 71.0 1.0 CZ A:PHE114 4.4 68.6 1.0 CE2 A:PHE114 4.5 68.1 1.0 CG1 A:VAL119 4.5 67.7 1.0 F1 A:VOR501 4.7 76.7 1.0 CA A:GLY290 4.8 68.6 1.0 CG2 A:VAL119 4.8 70.4 1.0 C2D A:HEM502 4.9 57.0 1.0

A.Debnath, C.M.Calvet, G.Jennings, W.Zhou, A.Aksenov, M.R.Luth, R.Abagyan, W.D.Nes, J.H.Mckerrow, L.M.Podust. CYP51 Is An Essential Drug Target For the Treatment of Primary Amoebic Meningoencephalitis (Pam). Plos Negl Trop Dis V. 11 06104 2017.
ISSN: ESSN 1935-2735
PubMed: 29284029
DOI: 10.1371/JOURNAL.PNTD.0006104