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Fluorine in PDB 4h4o: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor, PDB code: 4h4o was solved by K.M.Frey, K.S.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.72 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 225.451, 69.575, 104.401, 90.00, 106.21, 90.00
R / Rfree (%) 23.2 / 26.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor (pdb code 4h4o). 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 (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor, PDB code: 4h4o:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 4h4o

Go back to Fluorine Binding Sites List in 4h4o
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), 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 (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.8
occ:1.00
 FAD A:506601 0.0 0.8 1.0
CAV A:506601 1.3 0.4 1.0
CAI A:506601 2.3 0.6 1.0
CAO A:506601 2.4 0.5 1.0
CG2 A:VAL179 3.0 0.9 1.0
CE A:LYS103 3.4 0.4 1.0
CG A:LYS103 3.5 0.8 1.0
CAJ A:506601 3.6 0.7 1.0
CBA A:506601 3.6 0.4 1.0
CB A:VAL179 3.7 0.6 1.0
OH A:TYR181 4.0 0.2 1.0
CD A:LYS103 4.0 0.5 1.0
CAZ A:506601 4.1 1.0 1.0
CZ A:TYR181 4.3 0.6 1.0
O A:LYS101 4.3 0.4 1.0
CG1 A:VAL179 4.3 0.8 1.0
CE1 A:TYR181 4.5 0.3 1.0
CA A:GLY190 4.5 1.0 1.0
NZ A:LYS103 4.6 0.0 1.0
OAT A:506601 4.7 0.3 1.0
CB A:LYS103 4.9 0.2 1.0
CE2 A:TYR181 4.9 0.5 1.0
N A:GLY190 4.9 0.9 1.0

Fluorine binding site 2 out of 2 in 4h4o

Go back to Fluorine Binding Sites List in 4h4o
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), 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 (Rt) in Complex with (E)-3-(3-(2-(2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)Ethoxy)- 4- Fluorophenoxy)-5-Fluorophenyl)Acrylonitrile (JLJ506), A Non- Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:0.7
occ:1.00
 FAE A:506601 0.0 0.7 1.0
CAW A:506601 1.3 0.9 1.0
CAN A:506601 2.3 1.0 1.0
CAM A:506601 2.4 0.6 1.0
CD2 A:LEU100 3.4 0.9 1.0
CD1 A:LEU100 3.5 0.5 1.0
CG A:PRO95 3.6 0.6 1.0
CAY A:506601 3.6 0.2 1.0
CAX A:506601 3.6 0.1 1.0
CD1 A:TYR181 3.9 0.4 1.0
CH2 A:TRP229 4.0 0.0 1.0
CG A:LEU100 4.0 0.8 1.0
CAP A:506601 4.1 0.7 1.0
CZ3 A:TRP229 4.1 0.1 1.0
CB A:PRO95 4.2 0.9 1.0
CE1 A:TYR181 4.3 0.3 1.0
CZ2 A:TRP229 4.5 0.7 1.0
CD2 A:TYR188 4.7 0.6 1.0
OAU A:506601 4.8 1.0 1.0
CE3 A:TRP229 4.8 0.3 1.0
O A:PRO95 4.8 0.4 1.0
CAH A:506601 4.9 0.0 1.0
CD A:PRO95 4.9 0.1 1.0
CG A:TYR181 5.0 1.0 1.0

Reference:

K.M.Frey, M.Bollini, A.C.Mislak, J.A.Cisneros, R.Gallardo-Macias, W.L.Jorgensen, K.S.Anderson. Crystal Structures of Hiv-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions For Drug Design. J.Am.Chem.Soc. V. 134 19501 2012.
ISSN: ISSN 0002-7863
PubMed: 23163887
DOI: 10.1021/JA3092642
Page generated: Mon Jul 14 21:58:01 2025

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