Fluorine in PDB 6ea1: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion, PDB code: 6ea1 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)	54.46 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.491, 108.920, 118.150, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.1

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion (pdb code 6ea1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion, PDB code: 6ea1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:32.1 occ:0.90 FBA A:J0Y1102 0.0 32.1 0.9 CAZ A:J0Y1102 1.4 34.2 0.9 FBB A:J0Y1102 2.1 32.5 0.9 FBC A:J0Y1102 2.2 36.5 0.9 CAQ A:J0Y1102 2.4 16.7 0.9 CAP A:J0Y1102 2.8 12.2 0.9 FAY A:J0Y1102 2.9 20.1 0.9 N A:J0Y1102 3.3 10.0 0.9 OAR A:J0Y1102 3.4 9.8 0.9 CE1 A:HIS496 3.9 9.5 1.0 ND1 A:HIS496 3.9 9.8 1.0 NE2 A:HIS496 3.9 10.0 1.0 CG A:HIS496 4.0 9.7 1.0 CD2 A:HIS496 4.0 12.3 1.0 O A:HOH2173 4.3 24.0 1.0 C A:J0Y1102 4.3 7.6 0.9 CA A:J0Y1102 4.3 7.3 0.9 O A:J0Y1102 4.5 7.6 0.9 NAS A:J0Y1102 4.5 7.3 0.9 CE2 A:TYR580 4.6 11.1 1.0 OE2 A:GLU497 4.6 9.6 1.0 O A:HOH1239 4.7 11.0 1.0 CB A:HIS496 4.7 7.2 1.0 O A:HOH1997 4.8 27.5 1.0 CD2 A:TYR580 4.9 10.9 1.0 CG2 A:VAL493 4.9 10.1 1.0

Fluorine binding site 2 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:32.5 occ:0.90 FBB A:J0Y1102 0.0 32.5 0.9 CAZ A:J0Y1102 1.3 34.2 0.9 FBA A:J0Y1102 2.1 32.1 0.9 FBC A:J0Y1102 2.1 36.5 0.9 CAQ A:J0Y1102 2.3 16.7 0.9 OAR A:J0Y1102 2.8 9.8 0.9 CAP A:J0Y1102 2.9 12.2 0.9 O A:HOH1997 3.4 27.5 1.0 NH2 A:ARG489 3.4 15.7 1.0 FAY A:J0Y1102 3.5 20.1 0.9 NH1 A:ARG489 3.6 14.3 1.0 CZ A:ARG489 3.8 16.7 1.0 CG2 A:VAL493 3.8 10.1 1.0 N A:J0Y1102 4.0 10.0 0.9 CA A:GLY460 4.1 7.7 1.0 N A:GLY460 4.6 7.3 1.0 O A:HOH2101 4.6 22.4 1.0 CG1 A:VAL493 4.7 8.2 1.0 N A:ALA461 4.8 7.8 1.0 CB A:VAL493 4.8 7.9 1.0 NE A:ARG489 4.9 16.1 1.0 C A:GLY460 4.9 10.6 1.0

Fluorine binding site 3 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) 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 (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:36.5 occ:0.90 FBC A:J0Y1102 0.0 36.5 0.9 CAZ A:J0Y1102 1.4 34.2 0.9 FBB A:J0Y1102 2.1 32.5 0.9 FBA A:J0Y1102 2.2 32.1 0.9 CAQ A:J0Y1102 2.4 16.7 0.9 FAY A:J0Y1102 2.8 20.1 0.9 O A:HOH1997 3.1 27.5 1.0 O A:HOH2173 3.2 24.0 1.0 O A:HOH2240 3.3 49.2 1.0 CAP A:J0Y1102 3.7 12.2 0.9 NH1 A:ARG489 3.8 14.3 1.0 O A:HOH1412 3.9 18.3 1.0 OAR A:J0Y1102 4.3 9.8 0.9 N A:J0Y1102 4.6 10.0 0.9 O A:HOH2377 4.6 58.2 1.0 CZ A:ARG489 4.6 16.7 1.0 NH2 A:ARG489 4.6 15.7 1.0 O A:HOH1239 5.0 11.0 1.0

Fluorine binding site 4 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:20.1 occ:0.90 FAY A:J0Y1102 0.0 20.1 0.9 CAQ A:J0Y1102 1.4 16.7 0.9 CAP A:J0Y1102 2.3 12.2 0.9 CAZ A:J0Y1102 2.4 34.2 0.9 N A:J0Y1102 2.5 10.0 0.9 FBC A:J0Y1102 2.8 36.5 0.9 FBA A:J0Y1102 2.9 32.1 0.9 O A:HOH2377 3.2 58.2 1.0 O A:HOH2156 3.3 28.8 1.0 CE2 A:TYR580 3.3 11.1 1.0 OAR A:J0Y1102 3.5 9.8 0.9 FBB A:J0Y1102 3.5 32.5 0.9 O A:HOH2240 3.5 49.2 1.0 CD2 A:TYR580 3.6 10.9 1.0 CA A:J0Y1102 4.0 7.3 0.9 CZ A:TYR580 4.0 9.5 1.0 O A:HOH1997 4.0 27.5 1.0 O A:HOH2101 4.1 22.4 1.0 O A:HOH2162 4.2 29.2 1.0 CG A:TYR580 4.4 10.5 1.0 O A:HOH1412 4.4 18.3 1.0 O A:J0Y1102 4.5 7.6 0.9 OH A:TYR580 4.5 7.3 1.0 C A:J0Y1102 4.6 7.6 0.9 CAK A:J0Y1102 4.7 7.3 0.9 CE1 A:TYR580 4.8 8.7 1.0 CAJ A:J0Y1102 4.8 6.9 0.9 CD1 A:TYR580 5.0 11.1 1.0

Fluorine binding site 5 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:10.8 occ:0.90 FAV A:J0Y1102 0.0 10.8 0.9 CAA A:J0Y1102 1.3 9.6 0.9 CAF A:J0Y1102 2.3 10.2 0.9 CAB A:J0Y1102 2.3 7.5 0.9 FAW A:J0Y1102 2.8 10.8 0.9 O A:HOH1751 3.2 8.9 1.0 N A:ALA320 3.4 8.9 1.0 CA A:GLU572 3.5 17.9 1.0 CAE A:J0Y1102 3.6 7.9 0.9 CAC A:J0Y1102 3.6 7.9 0.9 CG A:GLU572 3.6 18.3 1.0 CE1 A:TYR575 3.7 9.4 1.0 O A:GLU319 3.7 10.0 1.0 O A:MET571 3.8 19.5 1.0 C A:GLU319 4.0 8.4 1.0 N A:GLU572 4.0 16.9 1.0 CB A:GLU572 4.0 18.2 1.0 CD1 A:TYR575 4.1 7.6 1.0 C A:MET571 4.1 16.6 1.0 CAD A:J0Y1102 4.1 7.5 0.9 CB A:ALA320 4.2 8.3 1.0 CZ A:TYR575 4.4 7.4 1.0 CA A:ALA320 4.4 8.4 1.0 C A:GLU572 4.5 20.8 1.0 CE A:MET1034 4.5 12.2 1.0 O A:GLU572 4.7 22.0 1.0 FAX A:J0Y1102 4.7 7.9 0.9 OH A:TYR575 4.7 9.0 1.0 CB A:MET571 4.8 18.6 1.0 SD A:MET1034 4.8 11.5 1.0 O A:HOH1512 4.8 12.7 1.0 CAG A:J0Y1102 4.8 7.2 0.9 CD A:GLU572 4.9 21.1 1.0 CG A:TYR575 5.0 8.0 1.0

Fluorine binding site 6 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:10.8 occ:0.90 FAW A:J0Y1102 0.0 10.8 0.9 CAF A:J0Y1102 1.4 10.2 0.9 CAE A:J0Y1102 2.4 7.9 0.9 CAA A:J0Y1102 2.4 9.6 0.9 FAX A:J0Y1102 2.7 7.9 0.9 FAV A:J0Y1102 2.8 10.8 0.9 CG A:GLU572 3.2 18.3 1.0 O A:HOH1512 3.2 12.7 1.0 O A:HOH1754 3.3 12.5 1.0 OE2 A:GLU572 3.4 19.6 1.0 CG2 A:THR305 3.5 9.5 1.0 O A:GLU319 3.5 10.0 1.0 O A:HOH1751 3.6 8.9 1.0 CD A:GLU572 3.6 21.1 1.0 SD A:MET1034 3.7 11.5 1.0 CAD A:J0Y1102 3.7 7.5 0.9 CAB A:J0Y1102 3.7 7.5 0.9 CAC A:J0Y1102 4.2 7.9 0.9 CB A:GLU572 4.2 18.2 1.0 C A:GLU319 4.4 8.4 1.0 CE A:MET1034 4.4 12.2 1.0 N A:ALA320 4.4 8.9 1.0 CB A:THR305 4.6 10.9 1.0 OE1 A:GLU572 4.6 21.5 1.0 CA A:GLU572 4.7 17.9 1.0

Fluorine binding site 7 out of 7 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6DA) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:7.9 occ:0.90 FAX A:J0Y1102 0.0 7.9 0.9 CAE A:J0Y1102 1.4 7.9 0.9 CAF A:J0Y1102 2.4 10.2 0.9 CAD A:J0Y1102 2.4 7.5 0.9 FAW A:J0Y1102 2.7 10.8 0.9 CG A:GLN317 3.3 8.2 1.0 O A:HOH2102 3.5 10.6 1.0 CG2 A:THR305 3.5 9.5 1.0 ND2 A:ASN458 3.5 8.1 1.0 CAA A:J0Y1102 3.7 9.6 0.9 SD A:MET1034 3.7 11.5 1.0 CAC A:J0Y1102 3.7 7.9 0.9 O A:GLU319 3.9 10.0 1.0 O A:HOH1754 3.9 12.5 1.0 CD A:GLN317 4.1 9.9 1.0 NE2 A:GLN317 4.1 8.0 1.0 CB A:ASN458 4.2 9.3 1.0 CE A:MET1034 4.2 12.2 1.0 CAB A:J0Y1102 4.2 7.5 0.9 O A:LEU304 4.2 10.7 1.0 CG A:ASN458 4.3 10.1 1.0 O A:HOH1702 4.4 9.9 1.0 CB A:GLN317 4.5 8.6 1.0 CB A:THR305 4.7 10.9 1.0 FAV A:J0Y1102 4.7 10.8 0.9 CAG A:J0Y1102 4.8 7.2 0.9

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