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Fluorine in PDB 8str: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), 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 (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor, PDB code: 8str was solved by K.Hollander, A.H.Chan, 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) 39.92 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.73, 74.04, 107.83, 90, 99.09, 90
R / Rfree (%) 24 / 26.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor (pdb code 8str). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor, PDB code: 8str:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8str

Go back to Fluorine Binding Sites List in 8str
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), 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 (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:64.3
occ:1.00
 F01 A:7N1601 0.0 64.3 1.0
CAL A:7N1601 1.4 60.1 1.0
CAM A:7N1601 2.4 68.1 1.0
CAK A:7N1601 2.4 62.0 1.0
CD2 A:LEU100 3.3 53.4 1.0
CB A:PRO95 3.6 49.8 1.0
CAH A:7N1601 3.6 63.7 1.0
CAJ A:7N1601 3.6 72.3 1.0
CG A:PRO95 4.0 57.0 1.0
CD1 A:LEU100 4.0 59.6 1.0
CAI A:7N1601 4.1 66.8 1.0
CG A:LEU100 4.2 56.5 1.0
SG A:CYS181 4.3 76.0 1.0
CB A:CYS181 4.5 61.8 1.0
CD2 A:TYR188 4.6 75.0 1.0
CH2 A:TRP229 4.8 67.7 1.0
CBB A:7N1601 4.8 76.8 1.0
O0A A:7N1601 4.8 57.0 1.0
CE2 A:TYR188 5.0 70.5 1.0
CD A:PRO95 5.0 65.5 1.0
CA A:PRO95 5.0 64.7 1.0

Fluorine binding site 2 out of 2 in 8str

Go back to Fluorine Binding Sites List in 8str
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C) Varient in Complex with 5-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl) Ethoxy)-4-Fluorophenoxy)-7-Fluoro-2-Naphthonitrile (JLJ636), A Non- Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:66.3
occ:1.00
 F02 A:7N1601 0.0 66.3 1.0
C01 A:7N1601 1.4 50.0 1.0
C00 A:7N1601 2.4 52.1 1.0
C02 A:7N1601 2.4 55.8 1.0
NZ A:LYS101 3.1 57.7 1.0
CB A:VAL179 3.3 64.3 1.0
CG1 A:VAL179 3.4 51.1 1.0
C05 A:7N1601 3.6 56.7 1.0
C03 A:7N1601 3.6 52.7 1.0
O A:VAL179 3.9 64.2 1.0
CA A:GLY190 4.0 69.2 1.0
C04 A:7N1601 4.1 53.4 1.0
CG2 A:VAL179 4.2 73.3 1.0
N A:GLY190 4.2 66.4 1.0
C A:VAL179 4.3 61.4 1.0
O A:GLY190 4.3 73.0 1.0
CA A:VAL179 4.3 64.3 1.0
CE A:LYS101 4.4 69.1 1.0
CD A:LYS103 4.4 62.6 1.0
C A:GLY190 4.4 71.0 1.0
CG A:LYS103 4.4 70.0 1.0
CE A:LYS103 4.5 66.5 1.0
CG A:LYS101 4.6 78.2 1.0
SG A:CYS181 4.8 76.0 1.0
O0B A:7N1601 4.8 59.9 1.0
N A:VAL179 4.9 71.3 1.0
O A:LYS101 4.9 66.0 1.0

Reference:

K.Hollander, A.H.Chan, K.M.Frey, O.Hunker, J.A.Ippolito, K.A.Spasov, Y.J.Yeh, W.L.Jorgensen, Y.C.Ho, K.S.Anderson. Exploring Novel Hiv-1 Reverse Transcriptase Inhibitors with Drug Resistant Mutants: A Double Mutant Surprise. Protein Sci. E4814 2023.
ISSN: ESSN 1469-896X
PubMed: 37861472
DOI: 10.1002/PRO.4814
Page generated: Wed Jul 16 08:18:17 2025

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