Fluorine in PDB 5y1h: Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide

Protein crystallography data

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1h was solved by A.K.Marapaka, Y.Zhang, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.66 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.564, 109.241, 112.518, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.1

Other elements in 5y1h:

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide (pdb code 5y1h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide, PDB code: 5y1h:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5y1h

Go back to Fluorine Binding Sites List in 5y1h
Fluorine binding site 1 out of 2 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1108

b:42.0
occ:1.00
F1 A:E8C1108 0.0 42.0 1.0
CG1 A:E8C1108 1.4 40.0 1.0
CD1 A:E8C1108 2.3 36.6 1.0
CB A:E8C1108 2.6 28.1 1.0
N A:E8C1108 3.2 29.9 1.0
CA A:E8C1108 3.2 32.0 1.0
O A:HOH1680 3.3 34.8 1.0
O A:HOH1604 3.3 32.6 1.0
C3 A:E8C1108 3.6 37.5 1.0
CG2 A:E8C1108 3.8 34.2 1.0
CG1 A:VAL459 4.0 24.0 1.0
C4 A:E8C1108 4.2 32.3 1.0
CB A:VAL459 4.3 19.7 1.0
C8 A:E8C1108 4.3 27.9 1.0
O A:HOH1722 4.4 28.2 1.0
F2 A:E8C1108 4.6 41.1 1.0
NE2 A:GLN1038 4.9 20.4 1.0
CA A:VAL459 5.0 17.7 1.0
N2 A:E8C1108 5.0 22.1 1.0

Fluorine binding site 2 out of 2 in 5y1h

Go back to Fluorine Binding Sites List in 5y1h
Fluorine binding site 2 out of 2 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido)-N-Hydroxy-4- Methylpentanamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1108

b:41.1
occ:1.00
F2 A:E8C1108 0.0 41.1 1.0
C3 A:E8C1108 1.3 37.5 1.0
CD1 A:E8C1108 2.3 36.6 1.0
C4 A:E8C1108 2.3 32.3 1.0
O A:HOH1719 3.1 28.4 1.0
CZ A:ARG997 3.3 18.8 1.0
NE A:ARG997 3.3 18.2 1.0
NH2 A:ARG997 3.4 21.8 1.0
CD A:ARG997 3.5 17.9 1.0
CG1 A:E8C1108 3.6 40.0 1.0
CG2 A:E8C1108 3.6 34.2 1.0
OE1 A:GLN1038 3.7 21.7 1.0
NH1 A:ARG997 4.0 20.2 1.0
O A:ASN458 4.0 16.6 1.0
CB A:E8C1108 4.1 28.1 1.0
CD A:GLN1038 4.1 18.7 1.0
NE2 A:GLN1038 4.2 20.4 1.0
O A:HOH1636 4.6 20.6 1.0
CA A:VAL459 4.6 17.7 1.0
F1 A:E8C1108 4.6 42.0 1.0
O A:HOH1744 4.8 30.5 1.0
C A:ASN458 5.0 15.9 1.0

Reference:

A.K.Marapaka, A.Addlagatta. Crystal Structure of Plasmodium Falciparum Aminopeptidase N in Complex with (S)-2-(3-(2,4-Difluorobenzyl)Ureido) -N-Hydroxy-4-Methylpentanamide To Be Published.
Page generated: Sun Dec 13 12:42:56 2020

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