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Magnesium in PDB 5ter: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor:
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 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor, PDB code: 5ter was solved by A.H.Chan, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.29 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.620, 74.200, 108.600, 90.00, 99.98, 90.00
R / Rfree (%) 23 / 26.7

Other elements in 5ter:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor (pdb code 5ter). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor, PDB code: 5ter:

Magnesium binding site 1 out of 1 in 5ter

Go back to Magnesium Binding Sites List in 5ter
Magnesium binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 5- Chloro-7-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-8-Methyl-2-Naphthonitrile (JLJ651), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:74.2
occ:1.00
OD1 A:ASP498 2.4 67.5 1.0
OD1 A:ASP443 2.4 61.4 1.0
OD2 A:ASP498 2.9 62.1 1.0
OE2 A:GLU478 3.0 81.8 1.0
CG A:ASP498 3.0 61.0 1.0
CG A:ASP443 3.3 69.3 1.0
NE2 A:GLN547 3.4 86.5 1.0
O A:GLY444 3.5 59.6 1.0
OE1 A:GLN547 3.7 95.8 1.0
OD2 A:ASP443 3.7 79.3 1.0
CG A:GLU478 3.8 58.1 1.0
CD A:GLU478 3.8 74.8 1.0
CD A:GLN547 3.9 97.2 1.0
N A:GLY444 4.1 52.4 1.0
CB A:ASP498 4.5 61.4 1.0
CB A:ASP443 4.6 59.2 1.0
C A:GLY444 4.6 59.3 1.0
CA A:ASP443 4.6 50.1 1.0
C A:ASP498 4.9 52.9 1.0
N A:SER499 4.9 41.3 1.0
C A:ASP443 4.9 53.8 1.0
CA A:GLY444 5.0 54.7 1.0

Reference:

W.G.Lee, A.H.Chan, K.A.Spasov, K.S.Anderson, W.L.Jorgensen. Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers As Potent Anti-Hiv Agents. Acs Med Chem Lett V. 7 1156 2016.
ISSN: ISSN 1948-5875
PubMed: 27994756
DOI: 10.1021/ACSMEDCHEMLETT.6B00390
Page generated: Mon Sep 30 04:49:18 2024

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