Fluorine in PDB 6ee2: X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion, PDB code: 6ee2 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)	44.77 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	174.183, 177.867, 229.645, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 24

The structure of X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion also contains other interesting chemical elements:

Zinc

(Zn)

12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion (pdb code 6ee2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 36 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion, PDB code: 6ee2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:29.8 occ:1.00 FAD A:J1V703 0.0 29.8 1.0 CAV A:J1V703 1.3 22.9 1.0 CBA A:J1V703 2.4 30.5 1.0 CAK A:J1V703 2.4 24.0 1.0 FAF A:J1V703 2.7 33.9 1.0 O A:ALA577 3.1 15.6 1.0 O A:HOH957 3.3 17.4 1.0 CD1 A:LEU492 3.6 24.5 1.0 CAW A:J1V703 3.6 33.0 1.0 CAY A:J1V703 3.6 25.7 1.0 CZ A:PHE583 3.8 23.1 1.0 CE1 A:PHE398 4.1 24.5 1.0 CG A:LEU492 4.1 20.1 1.0 CD2 A:LEU395 4.1 26.6 1.0 CAL A:J1V703 4.1 24.3 1.0 CE1 A:PHE583 4.1 22.2 1.0 CD2 A:LEU492 4.2 17.7 1.0 C A:ALA577 4.2 15.6 1.0 CZ A:PHE398 4.3 28.0 1.0 CA A:GLY578 4.4 9.9 1.0 FAE A:J1V703 4.7 33.1 1.0 CAX A:J1V703 4.8 23.5 1.0 N A:GLY578 4.8 12.1 1.0 CE2 A:PHE583 4.9 29.2 1.0 O A:GLY578 4.9 16.5 1.0 CAH A:J1V703 5.0 21.6 1.0 C A:GLY578 5.0 13.3 1.0

Fluorine binding site 2 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:33.9 occ:1.00 FAF A:J1V703 0.0 33.9 1.0 CBA A:J1V703 1.3 30.5 1.0 CAW A:J1V703 2.3 33.0 1.0 CAV A:J1V703 2.4 22.9 1.0 FAE A:J1V703 2.7 33.1 1.0 FAD A:J1V703 2.7 29.8 1.0 CZ A:PHE583 3.1 23.1 1.0 SD A:MET392 3.5 46.5 1.0 CAL A:J1V703 3.6 24.3 1.0 CAK A:J1V703 3.6 24.0 1.0 CE2 A:PHE583 3.7 29.2 1.0 CD1 A:LEU492 3.7 24.5 1.0 O4 A:SO4711 3.7 68.0 1.0 CD2 A:LEU395 3.8 26.6 1.0 CE1 A:PHE583 4.1 22.2 1.0 O3 A:SO4711 4.1 64.7 1.0 CAY A:J1V703 4.1 25.7 1.0 S A:SO4711 4.3 72.1 1.0 O1 A:SO4711 4.4 63.1 1.0 CG A:MET392 4.6 33.3 1.0 CE A:MET392 4.8 39.3 1.0 CB A:MET392 4.8 18.2 1.0 CG A:LEU492 4.9 20.1 1.0 CD2 A:PHE583 4.9 23.1 1.0 CD2 A:LEU492 5.0 17.7 1.0

Fluorine binding site 3 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F703 b:33.1 occ:1.00 FAE A:J1V703 0.0 33.1 1.0 CAW A:J1V703 1.4 33.0 1.0 CBA A:J1V703 2.3 30.5 1.0 CAL A:J1V703 2.4 24.3 1.0 FAF A:J1V703 2.7 33.9 1.0 CG A:MET392 3.2 33.3 1.0 CB A:MET392 3.2 18.2 1.0 SD A:MET392 3.3 46.5 1.0 O A:GLY390 3.4 27.8 1.0 CAV A:J1V703 3.6 22.9 1.0 CAY A:J1V703 3.7 25.7 1.0 CAK A:J1V703 4.1 24.0 1.0 O A:SER391 4.2 23.9 1.0 C A:SER391 4.3 26.7 1.0 CA A:MET392 4.4 19.0 1.0 N A:MET392 4.4 16.9 1.0 C A:GLY390 4.5 27.5 1.0 O A:HOH1114 4.6 34.4 1.0 O4 A:SO4711 4.7 68.0 1.0 FAD A:J1V703 4.7 29.8 1.0 CD2 A:LEU395 4.8 26.6 1.0 CA A:SER391 4.8 20.6 1.0 CD1 A:LEU492 4.8 24.5 1.0 CAX A:J1V703 4.8 23.5 1.0 CE A:MET392 4.8 39.3 1.0

Fluorine binding site 4 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:F703 b:28.0 occ:1.00 FAD B:J1V703 0.0 28.0 1.0 CAV B:J1V703 1.4 27.5 1.0 CBA B:J1V703 2.4 29.9 1.0 CAK B:J1V703 2.4 24.4 1.0 FAF B:J1V703 2.7 34.7 1.0 O B:ALA577 3.0 18.5 1.0 O B:HOH884 3.3 18.1 1.0 CD1 B:LEU492 3.6 20.5 1.0 CAW B:J1V703 3.7 29.8 1.0 CZ B:PHE583 3.7 19.4 1.0 CAY B:J1V703 3.7 26.8 1.0 C B:ALA577 4.1 14.6 1.0 CE1 B:PHE583 4.1 25.0 1.0 CG B:LEU492 4.2 19.7 1.0 CAL B:J1V703 4.2 25.6 1.0 CE1 B:PHE398 4.2 24.4 1.0 CZ B:PHE398 4.2 26.0 1.0 CD2 B:LEU395 4.2 26.5 1.0 CD2 B:LEU492 4.2 16.2 1.0 CA B:GLY578 4.3 11.0 1.0 N B:GLY578 4.7 13.8 1.0 O B:GLY578 4.8 15.7 1.0 FAE B:J1V703 4.8 33.5 1.0 CE2 B:PHE583 4.8 20.5 1.0 CAX B:J1V703 4.8 17.6 1.0 C B:GLY578 4.9 18.8 1.0

Fluorine binding site 5 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:F703 b:34.7 occ:1.00 FAF B:J1V703 0.0 34.7 1.0 CBA B:J1V703 1.3 29.9 1.0 CAW B:J1V703 2.4 29.8 1.0 CAV B:J1V703 2.4 27.5 1.0 FAD B:J1V703 2.7 28.0 1.0 FAE B:J1V703 2.8 33.5 1.0 CZ B:PHE583 3.1 19.4 1.0 SD B:MET392 3.4 51.6 1.0 CD1 B:LEU492 3.6 20.5 1.0 CAL B:J1V703 3.6 25.6 1.0 CE2 B:PHE583 3.6 20.5 1.0 CAK B:J1V703 3.6 24.4 1.0 CD2 B:LEU395 3.8 26.5 1.0 CE B:MET392 4.0 69.3 1.0 CE1 B:PHE583 4.1 25.0 1.0 CAY B:J1V703 4.1 26.8 1.0 O E:HOH1130 4.5 33.0 1.0 CG B:MET392 4.6 34.2 1.0 O B:HOH1022 4.8 39.8 1.0 CG B:LEU492 4.8 19.7 1.0 CB B:MET392 4.8 18.5 1.0 CD2 B:PHE583 4.9 16.4 1.0 CD2 B:LEU492 4.9 16.2 1.0

Fluorine binding site 6 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ B:F703 b:33.5 occ:1.00 FAE B:J1V703 0.0 33.5 1.0 CAW B:J1V703 1.4 29.8 1.0 CBA B:J1V703 2.4 29.9 1.0 CAL B:J1V703 2.5 25.6 1.0 FAF B:J1V703 2.8 34.7 1.0 CG B:MET392 3.2 34.2 1.0 CB B:MET392 3.2 18.5 1.0 SD B:MET392 3.3 51.6 1.0 O B:HOH1022 3.4 39.8 1.0 O B:GLY390 3.5 26.3 1.0 CAV B:J1V703 3.7 27.5 1.0 CAY B:J1V703 3.7 26.8 1.0 CE B:MET392 4.0 69.3 1.0 C B:SER391 4.2 18.8 1.0 O B:SER391 4.2 18.1 1.0 CAK B:J1V703 4.2 24.4 1.0 N B:MET392 4.3 16.9 1.0 CA B:MET392 4.4 21.3 1.0 C B:GLY390 4.4 28.2 1.0 CA B:SER391 4.7 17.1 1.0 CD1 B:LEU492 4.7 20.5 1.0 CD2 B:LEU395 4.8 26.5 1.0 FAD B:J1V703 4.8 28.0 1.0 CAX B:J1V703 4.9 17.6 1.0

Fluorine binding site 7 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory 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-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:F703 b:34.0 occ:1.00 FAD C:J1V703 0.0 34.0 1.0 CAV C:J1V703 1.4 33.0 1.0 CBA C:J1V703 2.4 36.9 1.0 CAK C:J1V703 2.4 28.0 1.0 FAF C:J1V703 2.8 38.1 1.0 O C:ALA577 3.1 17.4 1.0 O C:HOH933 3.4 15.5 1.0 CZ C:PHE583 3.6 18.7 1.0 CAW C:J1V703 3.7 34.5 1.0 CAY C:J1V703 3.7 29.8 1.0 CD1 C:LEU492 3.9 26.8 1.0 CE1 C:PHE583 4.0 20.4 1.0 CZ C:PHE398 4.1 29.1 1.0 CAL C:J1V703 4.1 26.5 1.0 CD2 C:LEU395 4.2 27.1 1.0 CE1 C:PHE398 4.2 24.5 1.0 C C:ALA577 4.2 15.0 1.0 CG C:LEU492 4.3 21.3 1.0 CD2 C:LEU492 4.3 18.8 1.0 CA C:GLY578 4.5 14.1 1.0 CE2 C:PHE583 4.8 22.6 1.0 FAE C:J1V703 4.8 33.5 1.0 O C:GLY578 4.8 16.4 1.0 CAX C:J1V703 4.8 20.6 1.0 N C:GLY578 4.8 13.9 1.0 C C:GLY578 5.0 14.9 1.0

Fluorine binding site 8 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:F703 b:38.1 occ:1.00 FAF C:J1V703 0.0 38.1 1.0 CBA C:J1V703 1.4 36.9 1.0 CAW C:J1V703 2.4 34.5 1.0 CAV C:J1V703 2.4 33.0 1.0 FAE C:J1V703 2.7 33.5 1.0 FAD C:J1V703 2.8 34.0 1.0 CZ C:PHE583 3.1 18.7 1.0 SD C:MET392 3.5 59.1 1.0 CE2 C:PHE583 3.6 22.6 1.0 CAL C:J1V703 3.7 26.5 1.0 CAK C:J1V703 3.7 28.0 1.0 CD2 C:LEU395 3.7 27.1 1.0 CD1 C:LEU492 3.8 26.8 1.0 CE1 C:PHE583 4.0 20.4 1.0 CAY C:J1V703 4.2 29.8 1.0 O D:HOH872 4.5 33.8 1.0 CG C:MET392 4.6 31.1 1.0 CE C:MET392 4.7 27.8 1.0 CD2 C:PHE583 4.8 24.8 1.0 CG C:LEU492 4.9 21.3 1.0 CB C:MET392 4.9 22.6 1.0 CD2 C:LEU492 4.9 18.8 1.0

Fluorine binding site 9 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ C:F703 b:33.5 occ:1.00 FAE C:J1V703 0.0 33.5 1.0 CAW C:J1V703 1.4 34.5 1.0 CBA C:J1V703 2.4 36.9 1.0 CAL C:J1V703 2.5 26.5 1.0 FAF C:J1V703 2.7 38.1 1.0 CG C:MET392 3.1 31.1 1.0 SD C:MET392 3.3 59.1 1.0 CB C:MET392 3.4 22.6 1.0 O C:GLY390 3.4 21.1 1.0 CAV C:J1V703 3.7 33.0 1.0 CAY C:J1V703 3.7 29.8 1.0 O C:SER391 4.2 16.6 1.0 C C:SER391 4.2 19.6 1.0 CAK C:J1V703 4.2 28.0 1.0 N C:MET392 4.4 14.9 1.0 C C:GLY390 4.5 22.4 1.0 CA C:MET392 4.5 16.3 1.0 CA C:SER391 4.7 18.6 1.0 CD1 C:LEU492 4.7 26.8 1.0 CD2 C:LEU395 4.8 27.1 1.0 FAD C:J1V703 4.8 34.0 1.0 CE C:MET392 4.8 27.8 1.0 O C:HOH1096 4.8 32.3 1.0 CAX C:J1V703 4.9 20.6 1.0

Fluorine binding site 10 out of 36 in the X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of X-Ray Crystal Structure of Pf-M17 in Complex with Inhibitor 6I and Regulatory Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ D:F703 b:32.9 occ:1.00 FAD D:J1V703 0.0 32.9 1.0 CAV D:J1V703 1.3 30.5 1.0 CBA D:J1V703 2.3 36.6 1.0 CAK D:J1V703 2.4 25.6 1.0 FAF D:J1V703 2.7 34.1 1.0 O D:ALA577 3.0 15.7 1.0 O D:HOH983 3.4 19.4 1.0 CD1 D:LEU492 3.6 23.8 1.0 CAW D:J1V703 3.6 34.4 1.0 CAY D:J1V703 3.6 28.1 1.0 CZ D:PHE583 3.7 24.0 1.0 CG D:LEU492 4.1 22.9 1.0 CAL D:J1V703 4.1 30.5 1.0 C D:ALA577 4.2 12.8 1.0 CD2 D:LEU395 4.2 26.1 1.0 CE1 D:PHE398 4.2 25.1 1.0 CE1 D:PHE583 4.2 20.4 1.0 CD2 D:LEU492 4.3 19.1 1.0 CZ D:PHE398 4.3 25.5 1.0 CA D:GLY578 4.4 13.7 1.0 O D:GLY578 4.7 17.2 1.0 FAE D:J1V703 4.8 39.5 1.0 N D:GLY578 4.8 11.9 1.0 CAX D:J1V703 4.8 25.1 1.0 CE2 D:PHE583 4.8 26.5 1.0 C D:GLY578 4.9 16.9 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