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Arsenic 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:

Fluorine (F) 1 atom

Arsenic Binding Sites:

The binding sites of Arsenic 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 Arsenic atom.
In total 2 binding sites of Arsenic where 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:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in 7wce

Go back to Arsenic Binding Sites List in 7wce
Arsenic binding site 1 out of 2 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 Arsenic with other atoms in the As 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:As65

b:37.5
occ:1.00
 AS A:CAF65 0.0 37.5 1.0
O1 A:CAF65 1.7 53.4 1.0
CE1 A:CAF65 2.0 41.3 1.0
SG A:CAF65 2.2 30.2 1.0
CB A:CAF65 3.0 34.6 1.0
ND2 A:ASN120 3.5 27.1 1.0
N A:CAF65 3.5 28.1 1.0
OD1 A:ASN120 3.6 40.5 1.0
CG A:ASN120 3.7 49.7 1.0
O A:HOH445 3.8 33.8 1.0
CA A:CAF65 3.8 27.1 1.0
CG A:GLU92 4.1 45.4 1.0
OE1 A:GLU92 4.1 45.0 1.0
C A:ASP64 4.2 32.3 1.0
CD A:GLU92 4.5 51.9 1.0
OG1 A:THR97 4.5 29.5 1.0
CB A:ASN120 4.7 31.9 1.0
CA A:ASP64 4.7 28.1 1.0
O A:ASP64 4.8 33.6 1.0
O A:HOH407 4.8 35.6 1.0
CG A:LEU74 4.9 40.0 1.0

Arsenic binding site 2 out of 2 in 7wce

Go back to Arsenic Binding Sites List in 7wce
Arsenic binding site 2 out of 2 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 Arsenic with other atoms in the As binding site number 2 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:As130

b:36.6
occ:1.00
 AS A:CAF130 0.0 36.6 1.0
O1 A:CAF130 1.7 49.5 1.0
CE1 A:CAF130 2.0 57.8 1.0
SG A:CAF130 2.2 28.2 1.0
CB A:CAF130 3.1 28.5 1.0
N A:GLN137 3.9 46.9 1.0
C A:LYS136 4.0 49.9 1.0
CB A:GLN137 4.0 55.1 1.0
CG2 A:ILE135 4.3 39.0 1.0
O A:ILE135 4.3 36.3 1.0
CA A:GLN137 4.3 50.8 1.0
CA A:LYS136 4.3 34.8 1.0
O A:HOH438 4.3 52.3 1.0
O A:LYS136 4.4 36.7 1.0
CA A:CAF130 4.4 23.2 1.0
C A:ILE135 4.5 34.6 1.0
O A:HOH449 4.5 55.7 1.0
CB A:ILE135 4.6 27.4 1.0
N A:LYS136 4.6 38.2 1.0
CG A:GLN137 4.8 60.4 1.0
CG1 A:VAL126 4.9 33.0 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: Wed Jul 10 13:52:23 2024

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