Fluorine in PDB 6ee4: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion, PDB code: 6ee4 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)	41.29 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.110, 108.860, 118.080, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 18.9

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

Magnesium	(Mg)	5 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) and Catalytic Zinc Ion (pdb code 6ee4). 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 (6M) and Catalytic Zinc Ion, PDB code: 6ee4:
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 (6M) 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 (6M) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:11.8 occ:1.00 FAM A:J4S1102 0.0 11.8 1.0 CAK A:J4S1102 1.3 10.6 1.0 CAJ A:J4S1102 2.3 9.6 1.0 CAL A:J4S1102 2.4 9.2 1.0 FAN A:J4S1102 2.7 13.3 1.0 O A:HOH1823 3.1 12.2 1.0 N A:ALA320 3.4 7.7 1.0 CA A:GLU572 3.5 14.1 1.0 CAI A:J4S1102 3.6 9.4 1.0 CAG A:J4S1102 3.6 8.5 1.0 CG A:GLU572 3.6 13.1 1.0 O A:GLU319 3.7 10.6 1.0 O A:MET571 3.8 13.3 1.0 CE1 A:TYR575 3.9 8.6 1.0 C A:GLU319 3.9 7.5 1.0 N A:GLU572 3.9 11.7 1.0 C A:MET571 4.0 9.3 1.0 CAH A:J4S1102 4.1 8.6 1.0 CB A:GLU572 4.1 14.1 1.0 CB A:ALA320 4.2 9.6 1.0 CD1 A:TYR575 4.3 11.1 1.0 CA A:ALA320 4.4 7.7 1.0 CE A:MET1034 4.5 12.8 1.0 CZ A:TYR575 4.5 10.1 1.0 O A:HOH1434 4.6 13.1 1.0 C A:GLU572 4.6 15.4 1.0 FAO A:J4S1102 4.7 10.9 1.0 SD A:MET1034 4.7 12.4 1.0 CB A:MET571 4.7 15.9 1.0 O A:GLU572 4.8 16.8 1.0 OH A:TYR575 4.8 11.8 1.0 CD A:GLU572 4.8 16.9 1.0 CAF A:J4S1102 4.8 9.8 1.0 O A:HOH1700 5.0 12.0 1.0

Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) 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 (6M) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:13.3 occ:1.00 FAN A:J4S1102 0.0 13.3 1.0 CAJ A:J4S1102 1.4 9.6 1.0 CAK A:J4S1102 2.4 10.6 1.0 CAI A:J4S1102 2.4 9.4 1.0 FAM A:J4S1102 2.7 11.8 1.0 FAO A:J4S1102 2.7 10.9 1.0 O A:HOH1434 3.2 13.1 1.0 CG A:GLU572 3.3 13.1 1.0 O A:HOH1700 3.3 12.0 1.0 OE2 A:GLU572 3.4 16.1 1.0 CG2 A:THR305 3.5 15.2 1.0 O A:GLU319 3.5 10.6 1.0 CD A:GLU572 3.6 16.9 1.0 SD A:MET1034 3.6 12.4 1.0 CAH A:J4S1102 3.6 8.6 1.0 O A:HOH1823 3.7 12.2 1.0 CAL A:J4S1102 3.7 9.2 1.0 CAG A:J4S1102 4.2 8.5 1.0 CB A:GLU572 4.3 14.1 1.0 CE A:MET1034 4.3 12.8 1.0 C A:GLU319 4.4 7.5 1.0 N A:ALA320 4.5 7.7 1.0 CB A:THR305 4.5 13.5 1.0 OE1 A:GLU572 4.6 16.7 1.0 CA A:GLU572 4.6 14.1 1.0 ND2 A:ASN458 5.0 11.0 1.0

Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6M) 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 (6M) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:10.9 occ:1.00 FAO A:J4S1102 0.0 10.9 1.0 CAI A:J4S1102 1.4 9.4 1.0 CAJ A:J4S1102 2.4 9.6 1.0 CAH A:J4S1102 2.4 8.6 1.0 FAN A:J4S1102 2.7 13.3 1.0 CG A:GLN317 3.3 9.1 1.0 ND2 A:ASN458 3.4 11.0 1.0 O A:HOH2234 3.5 8.8 1.0 CG2 A:THR305 3.5 15.2 1.0 CAK A:J4S1102 3.6 10.6 1.0 SD A:MET1034 3.7 12.4 1.0 CAG A:J4S1102 3.7 8.5 1.0 O A:HOH1700 4.0 12.0 1.0 O A:GLU319 4.0 10.6 1.0 O A:LEU304 4.1 9.2 1.0 CB A:ASN458 4.1 7.5 1.0 CD A:GLN317 4.2 10.1 1.0 CAL A:J4S1102 4.2 9.2 1.0 NE2 A:GLN317 4.2 8.5 1.0 CG A:ASN458 4.2 9.2 1.0 CE A:MET1034 4.3 12.8 1.0 O A:HOH1812 4.4 9.3 1.0 CB A:GLN317 4.5 9.6 1.0 CB A:THR305 4.7 13.5 1.0 FAM A:J4S1102 4.7 11.8 1.0 CAF A:J4S1102 4.8 9.8 1.0 CA A:THR305 5.0 9.9 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