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Fluorine in PDB 6x4c: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), 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 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor, PDB code: 6x4c was solved by A.H.Chan, V.N.Duong, J.A.Ippolito, W.L.Jorgensen, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.23 / 2.86
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.186, 74.110, 108.357, 90.00, 100.13, 90.00
R / Rfree (%) 22 / 25.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor (pdb code 6x4c). 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 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor, PDB code: 6x4c:

Fluorine binding site 1 out of 1 in 6x4c

Go back to Fluorine Binding Sites List in 6x4c
Fluorine binding site 1 out of 1 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), 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 7-(2- (2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)- 5,8-Dimethyl-2-Naphthonitrile (JLJ658), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:88.6
occ:1.00
 F33 A:UNS601 0.0 88.6 1.0
C01 A:UNS601 1.3 71.4 1.0
C00 A:UNS601 2.4 62.5 1.0
C02 A:UNS601 2.4 69.9 1.0
CB A:VAL179 3.1 83.7 1.0
CG1 A:VAL179 3.2 79.4 1.0
C03 A:UNS601 3.7 66.6 1.0
C05 A:UNS601 3.7 61.7 1.0
OH A:TYR181 3.7 84.9 1.0
CZ A:TYR181 3.7 82.9 1.0
CG2 A:VAL179 3.9 87.3 1.0
O A:VAL179 4.0 80.1 1.0
CE1 A:TYR181 4.1 87.7 1.0
C04 A:UNS601 4.1 62.6 1.0
CE A:LYS103 4.1 83.1 1.0
CE2 A:TYR181 4.1 78.7 1.0
CG A:LYS103 4.2 81.8 1.0
CA A:VAL179 4.3 86.6 1.0
C A:VAL179 4.3 80.5 1.0
CA A:GLY190 4.5 81.6 1.0
O A:GLY190 4.6 91.1 1.0
N A:GLY190 4.7 78.8 1.0
CD1 A:TYR181 4.7 84.9 1.0
CD A:LYS103 4.8 82.1 1.0
C A:GLY190 4.8 91.8 1.0
CD2 A:TYR181 4.8 78.0 1.0
N A:VAL179 4.9 90.9 1.0
O A:LYS101 4.9 70.9 1.0
O0B A:UNS601 4.9 62.1 1.0

Reference:

V.N.Duong, J.A.Ippolito, A.H.Chan, W.G.Lee, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Structural Investigation of 2-Naphthyl Phenyl Ether Inhibitors Bound to Wt and Y181C Reverse Transcriptase Highlights Key Features of the Nnrti Binding Site. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 32643196
DOI: 10.1002/PRO.3910
Page generated: Fri Aug 2 03:59:28 2024

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