Arsenic in PDB 5kgx: HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid

The structure of HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid, PDB code: 5kgx was solved by L.Feng, M.Kobe, M.Kvaratskhelia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.08 / 2.67
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.109, 72.109, 65.713, 90.00, 90.00, 120.00
R / Rfree (%)	19.1 / 24.4

The binding sites of Arsenic atom in the HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid (pdb code 5kgx). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid, PDB code: 5kgx:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As65 b:76.0 occ:1.00 AS A:CAF65 0.0 76.0 1.0 O1 A:CAF65 1.6 0.3 1.0 CE1 A:CAF65 2.0 68.3 1.0 CE2 A:CAF65 2.0 61.5 1.0 SG A:CAF65 2.2 67.6 1.0 CB A:CAF65 3.2 70.9 1.0 OD1 A:ASN120 3.7 65.4 1.0 ND2 A:ASN120 3.8 58.8 1.0 CG A:ASN120 3.8 70.0 1.0 N A:CAF65 3.8 54.4 1.0 CD1 A:LEU74 4.0 66.5 1.0 OE2 A:GLU92 4.0 95.1 1.0 CA A:CAF65 4.0 67.2 1.0 CD A:GLU92 4.1 88.4 1.0 CG A:GLU92 4.1 69.0 1.0 C A:ASP64 4.2 53.2 1.0 OG1 A:THR97 4.5 58.7 1.0 CB A:ASN120 4.6 67.4 1.0 O A:HOH407 4.6 59.3 1.0 O A:ASP64 4.7 60.2 1.0 OE1 A:GLU92 4.7 76.0 1.0 CA A:ASP64 4.8 52.5 1.0

Arsenic binding site 2 out of 2 in the HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of HIV1 Catalytic Core Domain in Complex with An Inhibitor (2~{S})-2-[3- (3,4-Dihydro-2~{H}-Chromen-6-Yl)-1-Methyl-Indol-2-Yl]-2-[(2- Methylpropan-2-Yl)Oxy]Ethanoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As130 b:79.4 occ:1.00 AS A:CAF130 0.0 79.4 1.0 O1 A:CAF130 1.6 75.5 1.0 CE2 A:CAF130 2.0 78.8 1.0 CE1 A:CAF130 2.0 70.3 1.0 SG A:CAF130 2.2 73.3 1.0 CB A:CAF130 3.3 64.4 1.0 CG2 A:ILE135 4.3 49.1 1.0 O A:ILE135 4.4 64.2 1.0 CA A:CAF130 4.5 58.9 1.0 CB A:GLN137 4.8 79.6 1.0 C A:LYS136 4.8 78.7 1.0 CD2 A:PHE121 4.8 73.9 1.0 CG A:PHE121 4.8 67.2 1.0 N A:GLN137 4.8 92.1 1.0 C A:ILE135 4.8 56.8 1.0 CB A:ILE135 4.8 62.3 1.0 CG1 A:VAL126 4.9 50.6 1.0 OE1 A:GLN137 4.9 73.8 1.0 O A:LYS136 4.9 74.8 1.0 CA A:GLN137 4.9 87.9 1.0 CB A:PHE121 4.9 67.2 1.0

P.A.Patel, N.Kvaratskhelia, Y.Mansour, J.Antwi, L.Feng, P.Koneru, M.J.Kobe, N.Jena, G.Shi, M.S.Mohamed, C.Li, J.J.Kessl, J.R.Fuchs. Indole-Based Allosteric Inhibitors of Hiv-1 Integrase. Bioorg.Med.Chem.Lett. V. 26 4748 2016.
ISSN: ESSN 1464-3405
PubMed: 27568085
DOI: 10.1016/J.BMCL.2016.08.037