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Fluorine in PDB 5vqq: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), 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 N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor, PDB code: 5vqq 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) 43.22 / 2.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.400, 73.500, 108.260, 90.00, 99.27, 90.00
R / Rfree (%) 22.5 / 25.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor (pdb code 5vqq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor, PDB code: 5vqq:

Fluorine binding site 1 out of 1 in 5vqq

Go back to Fluorine Binding Sites List in 5vqq
Fluorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with N-(6- Cyano-3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy) Phenoxy)-4-Methylnaphthalen-1-Yl)-2-Fluoro-N-Methylacetamide (JLJ683), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:79.0
occ:1.00
 F1 A:9JP601 0.0 79.0 1.0
C26 A:9JP601 1.3 72.9 1.0
C25 A:9JP601 2.4 80.4 1.0
O5 A:9JP601 2.6 83.1 1.0
CB A:TYR181 3.1 64.3 1.0
CB A:TYR183 3.3 81.4 1.0
C A:GLN182 3.5 76.0 1.0
O A:GLN182 3.6 83.0 1.0
N3 A:9JP601 3.6 77.3 1.0
N A:GLN182 3.6 69.2 1.0
C A:TYR181 3.7 67.1 1.0
N A:TYR183 3.7 74.3 1.0
CD2 A:TYR188 3.8 70.2 1.0
CA A:TYR181 4.0 69.3 1.0
CA A:TYR183 4.0 74.9 1.0
O A:TYR181 4.1 68.6 1.0
CA A:GLN182 4.1 71.0 1.0
CG A:TYR181 4.2 74.5 1.0
C17 A:9JP601 4.2 73.1 1.0
CE2 A:TYR188 4.3 75.2 1.0
CG A:TYR183 4.5 85.0 1.0
CD2 A:TYR181 4.6 75.3 1.0
CG A:TYR188 4.6 70.2 1.0
C18 A:9JP601 4.7 70.9 1.0
CB A:TYR188 4.8 65.7 1.0
C27 A:9JP601 4.8 75.4 1.0
C16 A:9JP601 4.8 73.0 1.0
CD1 A:TYR183 4.8 85.8 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: Thu Aug 1 16:14:02 2024

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