Arsenic in PDB 5kgw: HIV1 Catalytic Core Domain in Complex with 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 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: 5kgw 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)	29.18 / 2.34
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.196, 72.196, 65.981, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 24.1

The binding sites of Arsenic atom in the HIV1 Catalytic Core Domain in Complex with 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 5kgw). 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 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: 5kgw:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the HIV1 Catalytic Core Domain in Complex with 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 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:53.8 occ:1.00 AS A:CAF65 0.0 53.8 1.0 O1 A:CAF65 1.6 56.0 1.0 CE1 A:CAF65 2.0 52.3 1.0 CE2 A:CAF65 2.0 76.0 1.0 SG A:CAF65 2.2 50.6 1.0 CB A:CAF65 3.2 51.7 1.0 OD1 A:ASN120 3.7 55.4 1.0 N A:CAF65 3.7 41.5 1.0 CG A:ASN120 3.8 54.3 1.0 ND2 A:ASN120 3.8 45.0 1.0 OE1 A:GLU92 3.9 63.8 1.0 CG A:GLU92 4.0 53.7 1.0 CA A:CAF65 4.0 48.8 1.0 CD A:GLU92 4.2 62.0 1.0 C A:ASP64 4.2 44.2 1.0 O A:HOH420 4.3 51.9 1.0 OG1 A:THR97 4.4 39.9 1.0 CB A:ASN120 4.7 47.5 1.0 O A:ASP64 4.8 48.0 1.0 CA A:ASP64 4.8 39.7 1.0 O A:HOH413 4.9 52.3 1.0 CG A:LEU74 5.0 52.2 1.0

Arsenic binding site 2 out of 2 in the HIV1 Catalytic Core Domain in Complex with 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 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:60.5 occ:1.00 AS A:CAF130 0.0 60.5 1.0 O1 A:CAF130 1.6 52.6 1.0 CE1 A:CAF130 2.0 46.5 1.0 CE2 A:CAF130 2.0 57.7 1.0 SG A:CAF130 2.2 51.7 1.0 CB A:CAF130 3.2 44.1 1.0 N A:GLN137 4.4 56.4 1.0 CG2 A:ILE135 4.4 45.4 1.0 O A:ILE135 4.4 46.7 1.0 CB A:GLN137 4.4 56.9 1.0 C A:LYS136 4.5 55.1 1.0 CA A:GLN137 4.6 65.8 1.0 CA A:CAF130 4.6 44.6 1.0 O A:LYS136 4.7 54.2 1.0 CG1 A:VAL126 4.8 37.9 1.0 C A:ILE135 4.8 44.4 1.0 CB A:ILE135 4.9 50.2 1.0 CD2 A:PHE121 4.9 39.9 1.0 CG A:PHE121 4.9 45.4 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