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Chlorine in PDB 5vqt: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor, PDB code: 5vqt was solved by A.H.Chan, D.J.Czyzyk, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.21 / 2.56
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.503, 73.471, 108.503, 90.00, 99.54, 90.00
R / Rfree (%) 22.6 / 24.2

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor (pdb code 5vqt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor, PDB code: 5vqt:

Chlorine binding site 1 out of 1 in 5vqt

Go back to Chlorine Binding Sites List in 5vqt
Chlorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 2- Chloro-N-(6-Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)Phenoxy)-4-Methylnaphthalen-1-Yl)-N-Methylacetamide (JLJ686), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:0.0
occ:1.00
 CL1 A:9K7601 0.0 0.0 1.0
C26 A:9K7601 1.8 91.5 1.0
C25 A:9K7601 2.8 90.5 1.0
CB A:TYR183 3.3 96.8 1.0
CD2 A:TYR188 3.3 82.4 1.0
O5 A:9K7601 3.4 93.8 1.0
CB A:TYR181 3.6 73.0 1.0
N3 A:9K7601 3.7 86.6 1.0
CE2 A:TYR188 3.7 86.7 1.0
C17 A:9K7601 3.9 83.7 1.0
N A:TYR183 4.1 90.5 1.0
C22 A:9K7601 4.1 86.3 1.0
C16 A:9K7601 4.1 81.3 1.0
C A:GLN182 4.2 88.8 1.0
CG A:TYR188 4.3 80.5 1.0
C A:TYR181 4.3 74.3 1.0
CA A:TYR183 4.3 90.9 1.0
O A:GLN182 4.3 95.2 1.0
CG A:TYR183 4.3 95.9 1.0
N A:GLN182 4.4 74.9 1.0
O A:TYR181 4.5 75.3 1.0
CG A:TYR181 4.5 75.7 1.0
CA A:TYR181 4.6 79.1 1.0
CB A:TYR188 4.6 77.8 1.0
C18 A:9K7601 4.7 77.3 1.0
CA A:GLN182 4.8 83.0 1.0
CD2 A:TYR181 4.8 76.1 1.0
CZ A:TYR188 4.9 90.6 1.0
CD1 A:TYR183 4.9 95.0 1.0
C27 A:9K7601 4.9 81.0 1.0
C21 A:9K7601 5.0 84.5 1.0

Reference:

A.H.Chan, W.G.Lee, K.A.Spasov, J.A.Cisneros, S.N.Kudalkar, Z.O.Petrova, A.B.Buckingham, K.S.Anderson, W.L.Jorgensen. Covalent Inhibitors For Eradication of Drug-Resistant Hiv-1 Reverse Transcriptase: From Design to Protein Crystallography. Proc. Natl. Acad. Sci. V. 114 9725 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28827354
DOI: 10.1073/PNAS.1711463114
Page generated: Sat Jul 12 10:00:10 2025

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