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Fluorine in PDB 5tw3: Crystal Structure of Hiv-1 Reverse Transcriptase 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 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 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; 3.1.13.2; 3.1.26.13; 3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase 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: 5tw3 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) 41.38 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.445, 69.469, 104.547, 90.00, 106.04, 90.00
R / Rfree (%) 22.7 / 27.3

Other elements in 5tw3:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase 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 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 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 5tw3). 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 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: 5tw3:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5tw3

Go back to Fluorine Binding Sites List in 5tw3
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase 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 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:52.7
occ:1.00
 F01 A:7N1601 0.0 52.7 1.0
CAL A:7N1601 1.3 52.3 1.0
CAM A:7N1601 2.4 53.1 1.0
CAK A:7N1601 2.4 56.6 1.0
CG A:PRO95 3.3 50.1 1.0
CD1 A:TYR181 3.3 49.9 1.0
CD2 A:LEU100 3.4 43.9 1.0
CAH A:7N1601 3.6 55.1 1.0
CAJ A:7N1601 3.7 57.2 1.0
CE1 A:TYR181 3.7 54.7 1.0
CB A:PRO95 3.8 50.2 1.0
CD1 A:LEU100 3.9 47.1 1.0
CAI A:7N1601 4.2 54.7 1.0
CG A:LEU100 4.2 47.1 1.0
CH2 A:TRP229 4.4 51.6 1.0
CG A:TYR181 4.4 48.7 1.0
CD A:PRO95 4.7 47.5 1.0
CZ3 A:TRP229 4.8 56.2 1.0
CZ2 A:TRP229 4.8 53.3 1.0
CD2 A:TYR188 4.8 49.6 1.0
CB A:TYR181 4.8 42.2 1.0
O0A A:7N1601 4.8 44.0 1.0
CBB A:7N1601 4.9 55.5 1.0
O A:PRO95 4.9 53.4 1.0
CZ A:TYR181 5.0 52.0 1.0

Fluorine binding site 2 out of 2 in 5tw3

Go back to Fluorine Binding Sites List in 5tw3
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase 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 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:57.9
occ:1.00
 F02 A:7N1601 0.0 57.9 1.0
C01 A:7N1601 1.3 47.0 1.0
C00 A:7N1601 2.4 41.1 1.0
C02 A:7N1601 2.4 51.2 1.0
CB A:VAL179 3.2 43.4 1.0
CG1 A:VAL179 3.3 38.5 1.0
CG A:LYS103 3.5 56.7 1.0
C05 A:7N1601 3.7 44.4 1.0
C03 A:7N1601 3.7 50.0 1.0
CE A:LYS103 3.7 54.6 1.0
CG2 A:VAL179 3.9 48.5 1.0
CA A:GLY190 4.0 56.3 1.0
O A:VAL179 4.0 49.6 1.0
C04 A:7N1601 4.2 46.3 1.0
CD A:LYS103 4.2 60.9 1.0
N A:GLY190 4.3 54.7 1.0
C A:GLY190 4.4 59.1 1.0
O A:GLY190 4.4 58.9 1.0
CA A:VAL179 4.4 49.5 1.0
CZ A:TYR181 4.5 52.0 1.0
C A:VAL179 4.5 51.9 1.0
OH A:TYR181 4.5 60.6 1.0
CE1 A:TYR181 4.7 54.7 1.0
CB A:LYS103 4.7 57.4 1.0
O0B A:7N1601 4.9 49.5 1.0
CE2 A:TYR181 4.9 68.2 1.0
O A:LYS101 4.9 51.0 1.0
N A:VAL179 5.0 58.2 1.0

Reference:

S.N.Kudalkar, J.Beloor, A.H.Chan, W.G.Lee, W.L.Jorgensen, P.Kumar, K.S.Anderson. Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors For Treating Hiv Infection. Mol. Pharmacol. V. 91 383 2017.
ISSN: ESSN 1521-0111
PubMed: 28167742
DOI: 10.1124/MOL.116.107755
Page generated: Thu Aug 1 15:27:10 2024

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