Fluorine in PDB 6ee6: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion, PDB code: 6ee6 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)	37.78 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.550, 108.610, 117.790, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.8

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

Magnesium	(Mg)	3 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) and Catalytic Zinc Ion (pdb code 6ee6). 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 (6O) and Catalytic Zinc Ion, PDB code: 6ee6:
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 (6O) 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 (6O) 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:J4P1102 0.0 12.6 1.0 CAV A:J4P1102 1.4 9.2 1.0 CBA A:J4P1102 2.4 11.9 1.0 CAK A:J4P1102 2.5 9.5 1.0 FAF A:J4P1102 2.7 14.3 1.0 CG A:GLN317 3.3 10.1 1.0 CG2 A:THR305 3.4 11.5 1.0 O A:HOH2235 3.5 12.1 1.0 ND2 A:ASN458 3.5 12.1 1.0 CAW A:J4P1102 3.7 10.5 1.0 SD A:MET1034 3.7 14.1 1.0 CAY A:J4P1102 3.7 10.9 1.0 O A:HOH1695 3.9 13.9 1.0 O A:GLU319 4.0 10.5 1.0 O A:LEU304 4.1 11.4 1.0 CD A:GLN317 4.2 9.3 1.0 CAL A:J4P1102 4.2 11.3 1.0 NE2 A:GLN317 4.2 9.1 1.0 CB A:ASN458 4.2 9.7 1.0 CG A:ASN458 4.4 8.9 1.0 CE A:MET1034 4.4 14.9 1.0 O A:HOH1693 4.4 11.0 1.0 CB A:GLN317 4.5 10.2 1.0 CB A:THR305 4.6 10.6 1.0 FAE A:J4P1102 4.7 14.1 1.0 CAX A:J4P1102 4.8 11.9 1.0 CA A:THR305 4.9 10.0 1.0

Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) 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 (6O) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:14.1 occ:1.00 FAE A:J4P1102 0.0 14.1 1.0 CAW A:J4P1102 1.3 10.5 1.0 CBA A:J4P1102 2.3 11.9 1.0 CAL A:J4P1102 2.3 11.3 1.0 FAF A:J4P1102 2.7 14.3 1.0 O A:HOH1848 3.2 12.5 1.0 N A:ALA320 3.4 9.5 1.0 CA A:GLU572 3.5 16.6 1.0 CAV A:J4P1102 3.6 9.2 1.0 CAY A:J4P1102 3.6 10.9 1.0 CG A:GLU572 3.6 18.6 1.0 O A:MET571 3.7 17.7 1.0 CE2 A:TYR575 3.7 9.9 1.0 O A:GLU319 3.8 10.5 1.0 N A:GLU572 3.9 16.0 1.0 C A:GLU319 4.0 8.6 1.0 C A:MET571 4.0 13.3 1.0 CB A:GLU572 4.0 15.8 1.0 CAK A:J4P1102 4.0 9.5 1.0 CD2 A:TYR575 4.1 11.8 1.0 CB A:ALA320 4.2 11.6 1.0 CE A:MET1034 4.4 14.9 1.0 CA A:ALA320 4.4 10.3 1.0 CZ A:TYR575 4.4 9.1 1.0 C A:GLU572 4.5 20.5 1.0 FAD A:J4P1102 4.7 12.6 1.0 O A:GLU572 4.7 22.4 1.0 SD A:MET1034 4.7 14.1 1.0 O A:HOH1613 4.7 13.9 1.0 OH A:TYR575 4.8 11.0 1.0 CB A:MET571 4.8 16.7 1.0 CAX A:J4P1102 4.8 11.9 1.0 CD A:GLU572 4.8 22.9 1.0

Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6O) 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 (6O) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:14.3 occ:1.00 FAF A:J4P1102 0.0 14.3 1.0 CBA A:J4P1102 1.4 11.9 1.0 CAW A:J4P1102 2.4 10.5 1.0 CAV A:J4P1102 2.4 9.2 1.0 FAE A:J4P1102 2.7 14.1 1.0 FAD A:J4P1102 2.7 12.6 1.0 O A:HOH1613 3.2 13.9 1.0 CG A:GLU572 3.2 18.6 1.0 O A:HOH1695 3.4 13.9 1.0 OE2 A:GLU572 3.4 19.0 1.0 CG2 A:THR305 3.5 11.5 1.0 O A:GLU319 3.5 10.5 1.0 O A:HOH1848 3.6 12.5 1.0 CD A:GLU572 3.6 22.9 1.0 CAK A:J4P1102 3.6 9.5 1.0 CAL A:J4P1102 3.7 11.3 1.0 SD A:MET1034 3.7 14.1 1.0 CAY A:J4P1102 4.2 10.9 1.0 CB A:GLU572 4.2 15.8 1.0 CE A:MET1034 4.4 14.9 1.0 N A:ALA320 4.4 9.5 1.0 C A:GLU319 4.4 8.6 1.0 CB A:THR305 4.6 10.6 1.0 OE1 A:GLU572 4.6 18.7 1.0 CA A:GLU572 4.6 16.6 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