Fluorine in PDB 7wce: Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid

Enzymatic activity of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid

All present enzymatic activity of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid, PDB code: 7wce was solved by Y.Taoda, Y.Sekiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.69 / 1.85
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.401, 72.401, 65.776, 90, 90, 120
R / Rfree (%) 19.3 / 21.4

Other elements in 7wce:

The structure of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid (pdb code 7wce). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid, PDB code: 7wce:

Fluorine binding site 1 out of 1 in 7wce

Go back to Fluorine Binding Sites List in 7wce
Fluorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid


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 Hiv-1 Integrase Catalytic Core Domain in Complex with (2S)-2-(Tert-Butoxy)-2-(10-Fluoro-2-(2-Hydroxy-4-Methylphenyl)- 1,4-Dimethyl-5-(Methylsulfonyl)-5,6-Dihydrophenanthridin-3-Yl)Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:44.8
occ:1.00
 F19 A:8Z3303 0.0 44.8 1.0
C18 A:8Z3303 1.3 60.3 1.0
C20 A:8Z3303 2.3 55.9 1.0
C17 A:8Z3303 2.4 49.9 1.0
C11 A:8Z3303 2.6 33.5 1.0
C12 A:8Z3303 3.0 32.6 1.0
C10 A:8Z3303 3.2 33.5 1.0
CG2 A:THR124 3.3 39.8 1.0
N A:THR125 3.5 27.5 1.0
C21 A:8Z3303 3.6 57.2 1.0
C A:THR124 3.6 32.3 1.0
C16 A:8Z3303 3.6 50.1 1.0
CB A:THR124 3.6 36.5 1.0
CG2 A:THR125 3.7 32.1 1.0
CA A:THR125 3.7 29.9 1.0
O A:THR124 3.8 31.1 1.0
C22 A:8Z3303 4.1 59.3 1.0
CA A:THR124 4.2 33.8 1.0
C13 A:8Z3303 4.4 31.8 1.0
CB A:THR125 4.4 36.7 1.0
O A:HOH404 4.5 43.2 1.0
C09 A:8Z3303 4.5 28.8 1.0
C24 A:8Z3303 4.6 40.4 1.0
O07 A:8Z3303 4.7 29.0 1.0
CB A:ALA128 4.8 27.7 1.0
OG1 A:THR124 4.9 31.9 1.0
C15 A:8Z3303 4.9 46.9 1.0

Reference:

Y.Taoda, T.Akiyama, K.Tomita, M.Fujiwara-Kitamura, Y.Tamura, T.Kawasuji, E.Matsuoka, E.Akihisa, T.Seki, T.Yoshinaga. Discovery of Tricyclic Hiv-1 Integrase-Ledgf/P75 Allosteric Inhibitors By Intramolecular Direct Arylation Reaction. Bioorg.Med.Chem.Lett. V. 64 28664 2022.
ISSN: ESSN 1464-3405
PubMed: 35272008
DOI: 10.1016/J.BMCL.2022.128664
Page generated: Fri Aug 2 14:47:45 2024

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