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Fluorine in PDB 5e9q: Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174

Enzymatic activity of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174

All present enzymatic activity of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174:
2.1.1.56; 2.1.1.57; 2.7.7.48; 3.4.21.91; 3.6.1.15; 3.6.4.13;

Protein crystallography data

The structure of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174, PDB code: 5e9q was solved by K.Barral, G.Bricogne, A.Sharff, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.84 / 1.79
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 60.950, 183.470, 51.280, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174 (pdb code 5e9q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174, PDB code: 5e9q:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5e9q

Go back to Fluorine Binding Sites List in 5e9q
Fluorine binding site 1 out of 3 in the Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:36.5
occ:0.68
F2 A:5KY302 0.0 36.5 0.7
C12 A:5KY302 1.3 31.4 0.7
F A:5KY302 2.1 30.4 0.7
F1 A:5KY302 2.1 29.8 0.7
C11 A:5KY302 2.4 28.0 0.7
C10 A:5KY302 3.1 23.9 0.7
CG A:PRO108 3.3 27.4 1.0
C13 A:5KY302 3.3 29.5 0.7
CD A:PRO108 3.6 24.1 1.0
N A:PRO108 4.0 23.0 1.0
CB A:PRO108 4.1 23.3 1.0
CA A:PRO108 4.2 22.7 1.0
C9 A:5KY302 4.3 22.6 0.7
C14 A:5KY302 4.5 29.9 0.7
C A:GLY107 4.8 25.2 1.0
C8 A:5KY302 4.9 27.7 0.7

Fluorine binding site 2 out of 3 in 5e9q

Go back to Fluorine Binding Sites List in 5e9q
Fluorine binding site 2 out of 3 in the Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:30.4
occ:0.68
F A:5KY302 0.0 30.4 0.7
C12 A:5KY302 1.3 31.4 0.7
F2 A:5KY302 2.1 36.5 0.7
F1 A:5KY302 2.1 29.8 0.7
C11 A:5KY302 2.3 28.0 0.7
C10 A:5KY302 2.8 23.9 0.7
C13 A:5KY302 3.5 29.5 0.7
C9 A:5KY302 4.2 22.6 0.7
C14 A:5KY302 4.7 29.9 0.7
C8 A:5KY302 5.0 27.7 0.7

Fluorine binding site 3 out of 3 in 5e9q

Go back to Fluorine Binding Sites List in 5e9q
Fluorine binding site 3 out of 3 in the Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dengue 3 NS5 Methyltransferase Bound to S-Adenosyl Methionine and Molecule BF174 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:29.8
occ:0.68
F1 A:5KY302 0.0 29.8 0.7
C12 A:5KY302 1.3 31.4 0.7
F A:5KY302 2.1 30.4 0.7
F2 A:5KY302 2.1 36.5 0.7
C11 A:5KY302 2.4 28.0 0.7
C13 A:5KY302 2.7 29.5 0.7
C10 A:5KY302 3.6 23.9 0.7
C14 A:5KY302 4.1 29.9 0.7
O A:HOH700 4.4 61.6 1.0
CD A:PRO108 4.7 24.1 1.0
C9 A:5KY302 4.8 22.6 0.7
N A:PRO108 4.9 23.0 1.0
CG A:PRO108 4.9 27.4 1.0
C8 A:5KY302 5.0 27.7 0.7
N2 A:5KY302 5.0 27.3 0.7

Reference:

F.Benmansour, I.Trist, B.Coutard, E.Decroly, G.Querat, A.Brancale, K.Barral. Discovery of Novel Dengue Virus NS5 Methyltransferase Non-Nucleoside Inhibitors By Fragment-Based Drug Design. Eur.J.Med.Chem. V. 125 865 2016.
ISSN: ISSN 0223-5234
PubMed: 27750202
DOI: 10.1016/J.EJMECH.2016.10.007
Page generated: Sun Dec 13 12:21:26 2020

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