Arsenic in PDB 7d83: Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid

The structure of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid, PDB code: 7d83 was solved by S.Sugiyama, Y.Sekiguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.62 / 2.43
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.312, 72.312, 65.845, 90, 90, 120
R / Rfree (%)	22.4 / 27.8

The binding sites of Arsenic atom in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid (pdb code 7d83). 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 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid, PDB code: 7d83:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-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 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As65 b:39.9 occ:0.60 AS A:CAF65 0.0 39.9 0.6 O1 A:CAF65 1.7 38.5 0.6 CE1 A:CAF65 2.0 39.5 0.6 SG A:CAF65 2.2 39.6 0.6 CB A:CAF65 3.1 42.6 0.6 ND2 A:ASN120 3.5 44.2 1.0 OD1 A:ASN120 3.6 47.6 1.0 OE1 A:GLU92 3.7 61.7 1.0 CG A:ASN120 3.7 45.1 1.0 N A:CAF65 3.8 42.1 0.6 CA A:CAF65 4.0 42.5 0.6 CD A:GLU92 4.0 60.8 1.0 CG A:GLU92 4.2 58.3 1.0 O A:HOH409 4.2 31.7 1.0 C A:ASP64 4.3 41.2 1.0 OG1 A:THR97 4.6 39.6 1.0 CD2 A:LEU74 4.6 41.1 1.0 OE2 A:GLU92 4.7 62.2 1.0 CB A:ASN120 4.7 44.1 1.0 CG A:LEU74 4.7 40.7 1.0 O A:ASP64 4.8 40.6 1.0 CA A:ASP64 4.9 41.7 1.0

Arsenic binding site 2 out of 2 in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-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 2-(Tert-Butoxy)-2-(2-(3-Cyclohexylureido)-3,6-Dimethyl-5-(5- Methylchroman-6-Yl)Pyridin-4-Yl)Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As130 b:51.4 occ:1.00 AS A:CAF130 0.0 51.4 1.0 O1 A:CAF130 1.7 49.9 1.0 CE1 A:CAF130 2.0 48.2 1.0 SG A:CAF130 2.2 43.8 1.0 CB A:CAF130 3.1 41.5 1.0 O A:ILE135 4.2 50.9 1.0 N A:GLN137 4.3 59.5 1.0 C A:LYS136 4.4 57.2 1.0 CA A:CAF130 4.5 40.9 1.0 CG2 A:ILE135 4.5 47.7 1.0 CB A:GLN137 4.5 61.5 1.0 CA A:GLN137 4.5 61.4 1.0 O A:LYS136 4.6 56.6 1.0 C A:ILE135 4.6 51.1 1.0 CB A:ILE135 4.7 48.0 1.0 CA A:LYS136 4.9 56.5 1.0 CD2 A:PHE121 5.0 45.0 1.0 CG1 A:VAL126 5.0 42.8 1.0 N A:LYS136 5.0 53.8 1.0

S.Sugiyama, T.Akiyama, Y.Taoda, T.Iwaki, E.Matsuoka, E.Akihisa, T.Seki, T.Yoshinaga, T.Kawasuji. Discovery of Novel Hiv-1 Integrase-Ledgf/P75 Allosteric Inhibitors Based on A Pyridine Scaffold Forming An Intramolecular Hydrogen Bond. Bioorg.Med.Chem.Lett. V. 33 27742 2020.
ISSN: ESSN 1464-3405
PubMed: 33316407
DOI: 10.1016/J.BMCL.2020.127742