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Fluorine in PDB 8eye: Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ

Protein crystallography data

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ, PDB code: 8eye 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) 46.28 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.838, 109.294, 117.764, 90, 90, 90
R / Rfree (%) 15.6 / 19.1

Other elements in 8eye:

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ (pdb code 8eye). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ, PDB code: 8eye:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 8eye

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Fluorine binding site 1 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:15.5
occ:1.00
 F01 A:X4I1106 0.0 15.5 1.0
C02 A:X4I1106 1.4 13.9 1.0
C03 A:X4I1106 2.3 12.8 1.0
C32 A:X4I1106 2.4 16.1 1.0
F33 A:X4I1106 2.8 16.4 1.0
O A:HOH1701 3.1 14.8 1.0
CG A:GLU572 3.4 20.0 1.0
CA A:GLU572 3.4 18.6 1.0
N A:ALA320 3.5 13.0 1.0
C04 A:X4I1106 3.6 13.1 1.0
C30 A:X4I1106 3.6 14.3 1.0
CE1 A:TYR575 3.7 14.8 1.0
O A:GLU319 3.8 14.1 1.0
CB A:GLU572 3.9 18.9 1.0
O A:MET571 4.0 20.8 1.0
N A:GLU572 4.0 20.0 1.0
CD1 A:TYR575 4.0 12.8 1.0
C A:GLU319 4.0 12.7 1.0
C29 A:X4I1106 4.1 14.4 1.0
CB A:ALA320 4.1 13.4 1.0
C A:MET571 4.2 19.9 1.0
CE A:MET1034 4.3 16.8 1.0
CA A:ALA320 4.4 13.0 1.0
CZ A:TYR575 4.5 14.6 1.0
C A:GLU572 4.5 21.2 1.0
O A:GLU572 4.5 21.4 1.0
CD A:GLU572 4.6 23.6 1.0
O A:HOH1459 4.7 17.0 1.0
F31 A:X4I1106 4.7 14.5 1.0
OH A:TYR575 4.8 13.9 1.0
SD A:MET1034 4.9 14.0 1.0
OE2 A:GLU572 4.9 20.4 1.0
C05 A:X4I1106 4.9 13.7 1.0
CG A:TYR575 4.9 12.1 1.0

Fluorine binding site 2 out of 5 in 8eye

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Fluorine binding site 2 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:23.9
occ:1.00
 F19 A:X4I1106 0.0 23.9 1.0
C18 A:X4I1106 1.3 17.7 1.0
C17 A:X4I1106 2.3 16.1 1.0
C20 A:X4I1106 2.4 19.0 1.0
C A:THR576 2.7 13.2 1.0
N A:THR577 3.0 13.2 1.0
CA A:THR576 3.0 13.7 1.0
O A:THR576 3.0 11.2 1.0
N A:THR576 3.2 15.3 1.0
C A:TYR575 3.5 16.8 1.0
O A:TYR575 3.6 14.2 1.0
C16 A:X4I1106 3.6 17.0 1.0
C21 A:X4I1106 3.6 18.0 1.0
CA A:THR577 3.8 14.1 1.0
O A:HOH1286 3.8 31.1 1.0
CD1 A:TYR580 3.8 12.7 1.0
O A:HOH2277 4.0 53.5 1.0
C23 A:X4I1106 4.1 16.0 1.0
CG A:TYR580 4.2 14.2 1.0
O A:HOH1644 4.3 14.4 1.0
CE1 A:TYR580 4.4 13.7 1.0
CB A:TYR580 4.5 11.7 1.0
CB A:THR576 4.5 14.7 1.0
CA A:TYR575 4.6 15.6 1.0
CB A:THR577 4.6 16.4 1.0
F22 A:X4I1106 4.7 24.8 1.0
O A:DMS1103 4.7 40.1 1.0
O A:HOH2223 4.8 41.8 1.0
N15 A:X4I1106 4.8 13.9 1.0
CB A:TYR575 4.8 14.1 1.0
C A:THR577 4.9 12.6 1.0
CD2 A:TYR580 5.0 14.6 1.0

Fluorine binding site 3 out of 5 in 8eye

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Fluorine binding site 3 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:24.8
occ:1.00
 F22 A:X4I1106 0.0 24.8 1.0
C21 A:X4I1106 1.4 18.0 1.0
C20 A:X4I1106 2.4 19.0 1.0
C23 A:X4I1106 2.4 16.0 1.0
O A:HOH1866 3.0 18.4 1.0
CG1 A:VAL459 3.3 11.4 1.0
C18 A:X4I1106 3.6 17.7 1.0
C16 A:X4I1106 3.7 17.0 1.0
O A:HOH2089 3.8 34.3 1.0
O A:HOH1595 3.8 21.7 1.0
C06 A:X4I1106 3.9 15.9 1.0
CE A:MET1034 4.1 16.8 1.0
CB A:TYR575 4.1 14.1 1.0
C07 A:X4I1106 4.1 13.5 1.0
C17 A:X4I1106 4.2 16.1 1.0
O A:HOH1215 4.3 17.9 1.0
CB A:VAL459 4.3 12.4 1.0
O A:TYR575 4.4 14.2 1.0
NE2 A:GLN1038 4.4 16.5 1.0
F19 A:X4I1106 4.7 23.9 1.0
O A:HOH2223 4.9 41.8 1.0
O A:HOH1936 4.9 57.3 1.0
N15 A:X4I1106 4.9 13.9 1.0
C A:TYR575 5.0 16.8 1.0

Fluorine binding site 4 out of 5 in 8eye

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Fluorine binding site 4 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:14.5
occ:1.00
 F31 A:X4I1106 0.0 14.5 1.0
C30 A:X4I1106 1.4 14.3 1.0
C32 A:X4I1106 2.4 16.1 1.0
C29 A:X4I1106 2.4 14.4 1.0
F33 A:X4I1106 2.7 16.4 1.0
ND2 A:ASN458 3.3 12.8 1.0
CG A:GLN317 3.4 14.8 1.0
CG2 A:THR305 3.4 18.4 1.0
O A:HOH2059 3.5 14.6 1.0
C02 A:X4I1106 3.7 13.9 1.0
C04 A:X4I1106 3.7 13.1 1.0
SD A:MET1034 3.8 14.0 1.0
O A:HOH1395 3.9 16.0 1.0
O A:GLU319 4.0 14.1 1.0
CB A:ASN458 4.1 12.6 1.0
O A:LEU304 4.1 16.1 1.0
CG A:ASN458 4.2 13.5 1.0
C03 A:X4I1106 4.2 12.8 1.0
CD A:GLN317 4.2 16.5 1.0
NE2 A:GLN317 4.3 13.3 1.0
O A:HOH1685 4.4 14.5 1.0
CE A:MET1034 4.5 16.8 1.0
CB A:GLN317 4.6 13.3 1.0
CB A:THR305 4.6 19.6 1.0
F01 A:X4I1106 4.7 15.5 1.0
C05 A:X4I1106 4.9 13.7 1.0
CA A:THR305 5.0 15.6 1.0

Fluorine binding site 5 out of 5 in 8eye

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Fluorine binding site 5 out of 5 in the Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Falciparum M1 in Complex with Inhibitor 9AJ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1106

b:16.4
occ:1.00
 F33 A:X4I1106 0.0 16.4 1.0
C32 A:X4I1106 1.4 16.1 1.0
C30 A:X4I1106 2.4 14.3 1.0
C02 A:X4I1106 2.4 13.9 1.0
F31 A:X4I1106 2.7 14.5 1.0
F01 A:X4I1106 2.8 15.5 1.0
CG A:GLU572 3.1 20.0 1.0
O A:HOH1459 3.2 17.0 1.0
OE2 A:GLU572 3.3 20.4 1.0
O A:HOH1395 3.4 16.0 1.0
CG2 A:THR305 3.5 18.4 1.0
CD A:GLU572 3.5 23.6 1.0
O A:GLU319 3.6 14.1 1.0
C29 A:X4I1106 3.6 14.4 1.0
O A:HOH1701 3.6 14.8 1.0
C03 A:X4I1106 3.7 12.8 1.0
SD A:MET1034 3.8 14.0 1.0
C04 A:X4I1106 4.1 13.1 1.0
CB A:GLU572 4.3 18.9 1.0
CE A:MET1034 4.3 16.8 1.0
OE1 A:GLU572 4.5 22.0 1.0
C A:GLU319 4.5 12.7 1.0
N A:ALA320 4.5 13.0 1.0
CB A:THR305 4.6 19.6 1.0
CA A:GLU572 4.8 18.6 1.0
ND2 A:ASN458 4.9 12.8 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 18:25:48 2024

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