Zinc in PDB 8eyd: Plasmodium Falciparum M1 in Complex with Inhibitor 15AH

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 15AH, PDB code: 8eyd 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)	44.19 / 1.83
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.367, 109.095, 118.104, 90, 90, 90
R / Rfree (%)	15.5 / 19.3

The structure of Plasmodium Falciparum M1 in Complex with Inhibitor 15AH also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Zinc atom in the Plasmodium Falciparum M1 in Complex with Inhibitor 15AH (pdb code 8eyd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Plasmodium Falciparum M1 in Complex with Inhibitor 15AH, PDB code: 8eyd:

Zinc binding site 1 out of 1 in the Plasmodium Falciparum M1 in Complex with Inhibitor 15AH


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Plasmodium Falciparum M1 in Complex with Inhibitor 15AH within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:14.6 occ:1.00 OE1 A:GLU519 2.0 12.2 1.0 O24 A:X4O1102 2.1 14.7 0.4 O24 A:X4O1102 2.1 14.6 0.6 NE2 A:HIS496 2.2 14.2 1.0 O23 A:X4O1102 2.2 14.4 0.6 NE2 A:HIS500 2.2 14.8 1.0 O23 A:X4O1102 2.2 14.4 0.4 C21 A:X4O1102 2.8 15.5 0.4 CD A:GLU519 2.8 13.4 1.0 C21 A:X4O1102 2.8 15.5 0.6 N22 A:X4O1102 2.9 13.2 0.4 N22 A:X4O1102 2.9 13.1 0.6 OE2 A:GLU519 2.9 13.2 1.0 CD2 A:HIS496 3.1 12.9 1.0 CD2 A:HIS500 3.1 15.6 1.0 CE1 A:HIS496 3.2 14.1 1.0 CE1 A:HIS500 3.2 14.1 1.0 O A:HOH1230 3.4 13.3 1.0 OH A:TYR580 4.1 12.2 1.0 OE1 A:GLU463 4.1 14.1 1.0 CE2 A:TYR580 4.1 12.0 1.0 CG A:HIS496 4.2 12.2 1.0 C08 A:X4O1102 4.3 15.0 0.4 ND1 A:HIS496 4.3 14.2 1.0 CG A:HIS500 4.3 12.8 1.0 CG A:GLU519 4.3 12.4 1.0 C08 A:X4O1102 4.3 15.0 0.6 ND1 A:HIS500 4.3 12.5 1.0 OE1 A:GLU497 4.4 14.9 1.0 CZ A:TYR580 4.5 12.2 1.0 CD A:GLU463 4.7 15.8 1.0 N09 A:X4O1102 4.8 15.3 0.4 OE2 A:GLU497 4.8 13.0 1.0 N09 A:X4O1102 4.8 15.2 0.6 O A:HOH1892 4.8 30.8 1.0 OE2 A:GLU463 4.8 15.6 1.0 CB A:GLU519 4.9 12.0 1.0 CG2 A:THR522 4.9 14.3 1.0 CA A:GLU519 4.9 12.2 1.0 CD A:GLU497 5.0 15.0 1.0

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