Atomistry » Arsenic » PDB 5hrn-5o8x » 5kgx
Atomistry »
  Arsenic »
    PDB 5hrn-5o8x »
      5kgx »

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

Protein crystallography data

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

Arsenic Binding Sites:

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 5kgx

Go back to Arsenic Binding Sites List in 5kgx
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 5kgx

Go back to Arsenic Binding Sites List in 5kgx
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

Reference:

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
Page generated: Mon Jul 7 00:18:07 2025

Last articles

Ca in 5S5M
Ca in 5S5L
Ca in 5S5K
Ca in 5S5J
Ca in 5S5I
Ca in 5S5H
Ca in 5S5G
Ca in 5S5F
Ca in 5S5D
Ca in 5S5E
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy