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Fluorine in PDB 8stu: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), 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, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor, PDB code: 8stu was solved by K.Hollander, 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) 29.62 / 2.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.611, 73.983, 109.092, 90, 100.9, 90
R / Rfree (%) 22.6 / 28

Other elements in 8stu:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor (pdb code 8stu). 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, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor, PDB code: 8stu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8stu

Go back to Fluorine Binding Sites List in 8stu
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), 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, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:69.4
occ:1.00
 F07 A:H9Y602 0.0 69.4 1.0
C01 A:H9Y602 1.5 63.0 1.0
C00 A:H9Y602 2.5 55.9 1.0
C02 A:H9Y602 2.5 60.3 1.0
CG1 A:VAL179 3.2 75.2 1.0
CB A:VAL179 3.3 79.8 1.0
C05 A:H9Y602 3.7 62.6 1.0
C03 A:H9Y602 3.8 65.3 1.0
CE A:LYS103 3.8 81.5 1.0
CD A:LYS103 3.9 77.3 1.0
CG A:LYS103 3.9 82.8 1.0
CG2 A:VAL179 4.0 81.9 1.0
O A:GLY190 4.1 85.4 1.0
C04 A:H9Y602 4.2 64.3 1.0
O A:VAL179 4.3 81.1 1.0
CA A:GLY190 4.3 76.9 1.0
C A:GLY190 4.4 89.7 1.0
CA A:VAL179 4.5 80.1 1.0
O A:LYS101 4.5 70.8 1.0
N A:GLY190 4.6 72.7 1.0
C A:VAL179 4.7 80.9 1.0
CB A:LYS103 4.7 75.1 1.0
NZ A:LYS103 4.7 86.9 1.0
O0B A:H9Y602 4.9 61.6 1.0
C0D A:H9Y602 4.9 71.8 1.0

Fluorine binding site 2 out of 2 in 8stu

Go back to Fluorine Binding Sites List in 8stu
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), 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, V106A) Variant in Complex with 8-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin- 1(2H)-Yl)Ethoxy)-4-Fluorophenoxy)-6-Fluoroindolizine-2-Carbonitrile (JLJ578), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:77.6
occ:1.00
 F13 A:H9Y602 0.0 77.6 1.0
C0Y A:H9Y602 1.4 67.7 1.0
C0X A:H9Y602 2.4 62.6 1.0
C0Z A:H9Y602 2.4 73.1 1.0
CD2 A:LEU100 3.1 65.5 1.0
CB A:PRO95 3.5 56.8 1.0
N0W A:H9Y602 3.6 70.0 1.0
C0C A:H9Y602 3.7 59.5 1.0
CG A:PRO95 3.9 61.5 1.0
CD1 A:LEU100 4.0 69.9 1.0
SG A:CYS181 4.0 90.6 1.0
CG A:LEU100 4.1 65.3 1.0
C0V A:H9Y602 4.1 65.0 1.0
CB A:CYS181 4.2 72.2 1.0
CG B:GLU138 4.4 61.3 1.0
CD2 A:TYR188 4.8 75.0 1.0
C11 A:H9Y602 4.8 78.6 1.0
CB B:GLU138 4.9 70.8 1.0
O0A A:H9Y602 4.9 62.6 1.0
CH2 A:TRP229 5.0 82.7 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 08:18:53 2025

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