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Fluorine in PDB 8ez4: Plasmodium Falciparum M17 in Complex with Inhibitor 9AA

Enzymatic activity of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA

All present enzymatic activity of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA:
3.4.11.1;

Protein crystallography data

The structure of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA, PDB code: 8ez4 was solved by P.P.S.Calic, S.Mcgowan, C.T.Webb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.47 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 173.94, 176.6, 230.901, 90, 90, 90
R / Rfree (%) 17.7 / 21.6

Other elements in 8ez4:

The structure of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA also contains other interesting chemical elements:

Zinc (Zn) 24 atoms
Sodium (Na) 9 atoms

Fluorine Binding Sites:

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 Plasmodium Falciparum M17 in Complex with Inhibitor 9AA (pdb code 8ez4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 36 binding sites of Fluorine where determined in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA, PDB code: 8ez4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 36 in 8ez4

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Fluorine binding site 1 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:46.0
occ:1.00
 F24 A:X10701 0.0 46.0 1.0
C23 A:X10701 1.4 46.8 1.0
C25 A:X10701 2.4 47.3 1.0
C22 A:X10701 2.4 47.8 1.0
O A:HOH984 2.6 27.7 1.0
F26 A:X10701 2.7 41.6 0.1
O A:ALA577 3.2 24.8 1.0
CZ A:PHE398 3.5 46.6 1.0
CZ A:PHE583 3.5 25.4 1.0
CE2 A:PHE583 3.6 26.3 1.0
CE2 A:PHE398 3.6 32.5 1.0
C27 A:X10701 3.6 46.2 0.3
C21 A:X10701 3.6 47.0 1.0
C29 A:X10701 4.1 47.0 0.5
CE1 A:PHE398 4.4 36.4 1.0
C A:ALA577 4.5 26.5 1.0
CB A:TRP581 4.5 20.1 1.0
CD2 A:PHE398 4.7 37.5 1.0
F28 A:X10701 4.7 50.8 0.4
CD1 A:LEU492 4.8 33.9 1.0
CE1 A:PHE583 4.8 34.6 1.0
CE A:MET392 4.9 42.8 1.0
CD2 A:PHE583 4.9 30.1 1.0
C20 A:X10701 5.0 44.3 1.0
CA A:GLY578 5.0 23.9 1.0
O A:GLY578 5.0 19.9 1.0

Fluorine binding site 2 out of 36 in 8ez4

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Fluorine binding site 2 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:41.6
occ:0.07
 F26 A:X10701 0.0 41.6 0.1
C25 A:X10701 1.4 47.3 1.0
C27 A:X10701 2.4 46.2 0.3
C23 A:X10701 2.4 46.8 1.0
F24 A:X10701 2.7 46.0 1.0
F28 A:X10701 2.7 50.8 0.4
CZ A:PHE583 2.9 25.4 1.0
CE2 A:PHE583 3.1 26.3 1.0
CD1 A:LEU492 3.3 33.9 1.0
C29 A:X10701 3.6 47.0 0.5
C22 A:X10701 3.7 47.8 1.0
CE A:MET392 3.8 42.8 1.0
CD2 A:LEU492 3.9 24.6 1.0
O F:HOH1171 3.9 47.4 1.0
CE1 A:PHE583 4.0 34.6 1.0
SD A:MET392 4.1 60.2 1.0
C21 A:X10701 4.1 47.0 1.0
CG A:LEU492 4.2 32.2 1.0
O F:HOH1153 4.2 44.8 1.0
CD2 A:PHE583 4.3 30.1 1.0
O A:HOH984 4.7 27.7 1.0
CD1 A:PHE583 5.0 31.2 1.0

Fluorine binding site 3 out of 36 in 8ez4

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Fluorine binding site 3 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:50.8
occ:0.37
 F28 A:X10701 0.0 50.8 0.4
C27 A:X10701 1.4 46.2 0.3
C29 A:X10701 2.4 47.0 0.5
C25 A:X10701 2.4 47.3 1.0
F26 A:X10701 2.7 41.6 0.1
CD1 A:LEU492 2.9 33.9 1.0
CE A:MET392 3.0 42.8 1.0
C21 A:X10701 3.6 47.0 1.0
C23 A:X10701 3.6 46.8 1.0
SD A:MET392 4.0 60.2 1.0
C22 A:X10701 4.1 47.8 1.0
CG A:LEU492 4.2 32.2 1.0
O F:HOH1171 4.7 47.4 1.0
CB A:LEU492 4.7 23.2 1.0
CD2 A:LEU492 4.7 24.6 1.0
F24 A:X10701 4.7 46.0 1.0
C20 A:X10701 4.8 44.3 1.0
C08 A:X10701 4.8 52.2 1.0
C30 A:X10701 4.8 47.9 1.0
C09 A:X10701 4.9 54.4 1.0

Fluorine binding site 4 out of 36 in 8ez4

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Fluorine binding site 4 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1401

b:82.5
occ:1.00
 F24 B:X101401 0.0 82.5 1.0
C23 B:X101401 1.4 72.2 1.0
C22 B:X101401 2.4 60.3 1.0
C25 B:X101401 2.4 68.8 1.0
F26 B:X101401 2.8 70.0 1.0
CD1 B:LEU492 2.9 37.9 1.0
SD B:MET392 3.2 80.1 1.0
C21 B:X101401 3.6 53.5 1.0
C27 B:X101401 3.7 46.0 1.0
CE B:MET392 3.9 58.9 1.0
C29 B:X101401 4.2 44.2 1.0
CG B:LEU492 4.3 24.5 1.0
CE E:LYS552 4.6 51.1 1.0
CG B:MET392 4.6 60.7 1.0
C07 B:X101401 4.6 41.3 1.0
C20 B:X101401 4.7 41.9 1.0
C19 B:X101401 4.7 48.7 1.0
O B:GLY390 4.7 37.1 1.0
F28 B:X101401 4.8 49.4 1.0
O E:HOH1130 4.9 46.0 1.0

Fluorine binding site 5 out of 36 in 8ez4

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Fluorine binding site 5 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1401

b:70.0
occ:1.00
 F26 B:X101401 0.0 70.0 1.0
C25 B:X101401 1.4 68.8 1.0
C23 B:X101401 2.4 72.2 1.0
C27 B:X101401 2.4 46.0 1.0
F28 B:X101401 2.7 49.4 1.0
F24 B:X101401 2.8 82.5 1.0
CZ B:PHE583 2.9 33.9 1.0
CD1 B:LEU492 3.1 37.9 1.0
CE2 B:PHE583 3.2 33.8 1.0
SD B:MET392 3.4 80.1 1.0
C22 B:X101401 3.6 60.3 1.0
C29 B:X101401 3.7 44.2 1.0
O E:HOH1130 3.7 46.0 1.0
CE1 B:PHE583 3.9 35.3 1.0
CE B:MET392 3.9 58.9 1.0
CD2 B:LEU492 4.0 25.3 1.0
CG B:LEU492 4.0 24.5 1.0
C21 B:X101401 4.1 53.5 1.0
CD2 B:PHE583 4.4 22.6 1.0
CD1 B:PHE583 4.9 36.6 1.0
O B:HOH1652 4.9 30.2 1.0

Fluorine binding site 6 out of 36 in 8ez4

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Fluorine binding site 6 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1401

b:49.4
occ:1.00
 F28 B:X101401 0.0 49.4 1.0
C27 B:X101401 1.4 46.0 1.0
C25 B:X101401 2.4 68.8 1.0
C29 B:X101401 2.4 44.2 1.0
O B:HOH1652 2.7 30.2 1.0
F26 B:X101401 2.7 70.0 1.0
O B:ALA577 3.1 27.5 1.0
CZ B:PHE583 3.3 33.9 1.0
O B:HOH1791 3.5 36.1 1.0
CE2 B:PHE583 3.6 33.8 1.0
C21 B:X101401 3.6 53.5 1.0
C23 B:X101401 3.6 72.2 1.0
CZ B:PHE398 3.9 33.8 1.0
C22 B:X101401 4.1 60.3 1.0
CE2 B:PHE398 4.2 36.0 0.7
CE B:MET392 4.3 58.9 1.0
C B:ALA577 4.3 29.4 1.0
CE1 B:PHE583 4.6 35.3 1.0
CE1 B:PHE398 4.6 31.3 0.6
CB B:TRP581 4.6 25.4 1.0
CA B:GLY578 4.8 24.0 1.0
F24 B:X101401 4.8 82.5 1.0
CD1 B:LEU492 4.8 37.9 1.0
CD2 B:LEU492 4.8 25.3 1.0
SD B:MET392 4.9 80.1 1.0
O B:GLY578 4.9 28.3 1.0
CD2 B:PHE583 5.0 22.6 1.0
C20 B:X101401 5.0 41.9 1.0

Fluorine binding site 7 out of 36 in 8ez4

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Fluorine binding site 7 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:37.4
occ:0.22
 F24 C:X10701 0.0 37.4 0.2
C23 C:X10701 1.4 41.6 1.0
C25 C:X10701 2.4 42.0 1.0
C22 C:X10701 2.4 39.9 0.7
O C:HOH958 2.7 30.5 1.0
F26 C:X10701 2.8 38.8 0.0
O C:ALA577 2.8 23.4 1.0
CE2 C:PHE398 3.1 35.7 1.0
CZ C:PHE398 3.4 46.8 1.0
C27 C:X10701 3.6 40.1 0.0
C21 C:X10701 3.6 39.4 0.5
CZ C:PHE583 3.8 33.2 1.0
CE2 C:PHE583 4.0 30.7 1.0
C C:ALA577 4.0 27.8 1.0
C29 C:X10701 4.1 42.0 0.8
CD2 C:PHE398 4.1 44.6 1.0
CB C:TRP581 4.5 20.1 1.0
CE1 C:PHE398 4.5 33.1 1.0
CA C:GLY578 4.8 25.1 1.0
F28 C:X10701 4.8 40.8 0.0
N C:GLY578 4.9 19.5 1.0
O C:GLY578 4.9 22.3 1.0
N C:TRP581 4.9 20.0 1.0
CA C:ALA577 5.0 22.4 1.0
C20 C:X10701 5.0 36.0 1.0
C C:GLY578 5.0 25.2 1.0

Fluorine binding site 8 out of 36 in 8ez4

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Fluorine binding site 8 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:38.8
occ:0.00
 F26 C:X10701 0.0 38.8 0.0
C25 C:X10701 1.4 42.0 1.0
C27 C:X10701 2.4 40.1 0.0
C23 C:X10701 2.4 41.6 1.0
F28 C:X10701 2.8 40.8 0.0
F24 C:X10701 2.8 37.4 0.2
CZ C:PHE583 2.8 33.2 1.0
CE2 C:PHE583 3.0 30.7 1.0
CD1 C:LEU492 3.2 34.5 1.0
C29 C:X10701 3.6 42.0 0.8
C22 C:X10701 3.7 39.9 0.7
CG C:LEU492 3.9 26.1 1.0
CE1 C:PHE583 3.9 34.7 1.0
CD2 C:LEU492 4.0 29.2 1.0
SD C:MET392 4.0 55.1 1.0
C21 C:X10701 4.1 39.4 0.5
CE C:MET392 4.2 39.9 1.0
CD2 C:PHE583 4.3 30.5 1.0
O C:HOH958 4.3 30.5 1.0
O D:HOH1184 4.5 47.8 1.0
O C:ALA577 4.5 23.4 1.0
CD1 C:PHE583 5.0 33.3 1.0

Fluorine binding site 9 out of 36 in 8ez4

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Fluorine binding site 9 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:40.8
occ:0.00
 F28 C:X10701 0.0 40.8 0.0
C27 C:X10701 1.4 40.1 0.0
C29 C:X10701 2.3 42.0 0.8
C25 C:X10701 2.4 42.0 1.0
CD1 C:LEU492 2.6 34.5 1.0
F26 C:X10701 2.8 38.8 0.0
CE C:MET392 2.8 39.9 1.0
C21 C:X10701 3.6 39.4 0.5
SD C:MET392 3.6 55.1 1.0
C23 C:X10701 3.6 41.6 1.0
CG C:LEU492 3.7 26.1 1.0
O C:HOH1122 3.9 52.8 1.0
C22 C:X10701 4.1 39.9 0.7
C09 C:X10701 4.5 51.8 1.0
CB C:LEU492 4.5 19.2 1.0
C20 C:X10701 4.7 36.0 1.0
CD2 C:LEU492 4.7 29.2 1.0
C19 C:X10701 4.7 41.6 1.0
F24 C:X10701 4.8 37.4 0.2
CG C:MET392 4.9 36.8 1.0

Fluorine binding site 10 out of 36 in 8ez4

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Fluorine binding site 10 out of 36 in the Plasmodium Falciparum M17 in Complex with Inhibitor 9AA


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Plasmodium Falciparum M17 in Complex with Inhibitor 9AA within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F701

b:36.9
occ:0.00
 F24 D:X10701 0.0 36.9 0.0
C23 D:X10701 1.4 51.6 1.0
O D:HOH1125 1.9 49.1 1.0
C25 D:X10701 2.3 33.7 1.0
C22 D:X10701 2.4 49.8 1.0
O D:HOH920 2.4 29.3 1.0
F26 D:X10701 2.7 33.0 0.3
CZ D:PHE398 2.9 48.5 1.0
O D:ALA577 2.9 22.8 1.0
CE1 D:PHE398 3.2 36.8 1.0
CE2 D:PHE398 3.4 39.6 1.0
C27 D:X10701 3.6 50.1 1.0
C21 D:X10701 3.6 44.1 1.0
CD1 D:PHE398 3.8 32.5 1.0
CD2 D:PHE398 4.0 39.7 1.0
C29 D:X10701 4.0 47.7 1.0
C D:ALA577 4.1 26.0 1.0
CB D:TRP581 4.2 26.1 1.0
CG D:PHE398 4.3 31.8 1.0
N D:TRP581 4.6 18.7 1.0
F28 D:X10701 4.7 38.9 0.3
CZ D:PHE583 4.7 32.2 1.0
CA D:ALA577 4.7 19.3 1.0
C20 D:X10701 4.9 43.5 1.0
CB D:SER580 5.0 24.2 1.0
CE2 D:PHE583 5.0 33.7 1.0

Reference:

P.P.S.Calic, N.B.Vinh, C.T.Webb, T.R.Malcolm, A.Ngo, K.Lowes, N.Drinkwater, S.Mcgowan, P.J.Scammells. Structure-Based Development of Potent Plasmodium Falciparum M1 and M17 Aminopeptidase Selective and Dual Inhibitors Via S1'-Region Optimisation Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
Page generated: Fri Aug 2 18:25:50 2024

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