Fluorine in PDB 6eed: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.80 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.149, 109.230, 117.920, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion (pdb code 6eed). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:12.6 occ:1.00 FAD A:J6A1102 0.0 12.6 1.0 CAW A:J6A1102 1.3 11.7 1.0 CBB A:J6A1102 2.3 12.2 1.0 CAK A:J6A1102 2.4 12.0 1.0 FAF A:J6A1102 2.7 14.7 1.0 O A:HOH1839 3.1 14.2 1.0 N A:ALA320 3.4 10.1 1.0 CG A:GLU572 3.5 15.2 1.0 CA A:GLU572 3.5 14.0 1.0 CAX A:J6A1102 3.6 10.4 1.0 CAZ A:J6A1102 3.6 11.7 1.0 O A:GLU319 3.7 10.6 1.0 CE1 A:TYR575 3.8 12.7 1.0 C A:GLU319 3.9 9.4 1.0 N A:GLU572 4.0 15.1 1.0 CB A:GLU572 4.0 12.8 1.0 O A:MET571 4.1 15.7 1.0 CD1 A:TYR575 4.1 10.6 1.0 CAL A:J6A1102 4.1 9.8 1.0 CB A:ALA320 4.2 11.1 1.0 C A:MET571 4.3 14.8 1.0 CA A:ALA320 4.4 10.6 1.0 CE A:MET1034 4.5 13.1 1.0 CZ A:TYR575 4.5 11.2 1.0 O A:HOH1540 4.5 14.4 1.0 C A:GLU572 4.6 15.1 1.0 O A:GLU572 4.7 17.4 1.0 CD A:GLU572 4.7 17.1 1.0 FAE A:J6A1102 4.7 12.2 1.0 SD A:MET1034 4.8 15.8 1.0 CAY A:J6A1102 4.9 11.3 1.0 OH A:TYR575 4.9 12.0 1.0 O A:HOH1712 4.9 13.9 1.0 OE2 A:GLU572 4.9 16.5 1.0 CG A:TYR575 5.0 9.8 1.0

Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:14.7 occ:1.00 FAF A:J6A1102 0.0 14.7 1.0 CBB A:J6A1102 1.4 12.2 1.0 CAX A:J6A1102 2.4 10.4 1.0 CAW A:J6A1102 2.4 11.7 1.0 FAD A:J6A1102 2.7 12.6 1.0 FAE A:J6A1102 2.7 12.2 1.0 O A:HOH1540 3.1 14.4 1.0 CG A:GLU572 3.3 15.2 1.0 OE2 A:GLU572 3.3 16.5 1.0 O A:HOH1712 3.3 13.9 1.0 CG2 A:THR305 3.4 12.0 1.0 CD A:GLU572 3.5 17.1 1.0 O A:GLU319 3.6 10.6 1.0 CAL A:J6A1102 3.6 9.8 1.0 O A:HOH1839 3.7 14.2 1.0 CAK A:J6A1102 3.7 12.0 1.0 SD A:MET1034 3.8 15.8 1.0 CAZ A:J6A1102 4.2 11.7 1.0 CB A:GLU572 4.4 12.8 1.0 CE A:MET1034 4.4 13.1 1.0 CB A:THR305 4.5 11.9 1.0 C A:GLU319 4.5 9.4 1.0 N A:ALA320 4.5 10.1 1.0 OE1 A:GLU572 4.5 16.4 1.0 CA A:GLU572 4.8 14.0 1.0

Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:12.2 occ:1.00 FAE A:J6A1102 0.0 12.2 1.0 CAX A:J6A1102 1.4 10.4 1.0 CBB A:J6A1102 2.4 12.2 1.0 CAL A:J6A1102 2.4 9.8 1.0 FAF A:J6A1102 2.7 14.7 1.0 CG2 A:THR305 3.4 12.0 1.0 CG A:GLN317 3.4 9.9 1.0 ND2 A:ASN458 3.4 12.1 1.0 O A:HOH2245 3.4 12.6 1.0 CAW A:J6A1102 3.7 11.7 1.0 SD A:MET1034 3.7 15.8 1.0 CAZ A:J6A1102 3.7 11.7 1.0 O A:HOH1712 4.0 13.9 1.0 O A:LEU304 4.1 12.5 1.0 CB A:ASN458 4.1 9.8 1.0 O A:GLU319 4.2 10.6 1.0 CAK A:J6A1102 4.2 12.0 1.0 CG A:ASN458 4.2 9.9 1.0 CD A:GLN317 4.3 10.5 1.0 O A:HOH1679 4.3 10.7 1.0 NE2 A:GLN317 4.3 10.7 1.0 CE A:MET1034 4.4 13.1 1.0 CB A:GLN317 4.6 9.1 1.0 CB A:THR305 4.6 11.9 1.0 FAD A:J6A1102 4.7 12.6 1.0 CAY A:J6A1102 4.8 11.3 1.0 CA A:THR305 4.9 11.5 1.0 C A:LEU304 5.0 11.0 1.0

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310