Fluorine in PDB 8sts: Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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, V106A) 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, V106A) 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, V106A) 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: 8sts 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) 38.11 / 3.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.86, 128.26, 133.042, 90, 105.32, 90
R / Rfree (%) 24 / 28.5

Other elements in 8sts:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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 8sts). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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: 8sts:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8sts

Go back to Fluorine Binding Sites List in 8sts
Fluorine binding site 1 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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, V106A) 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
C:F601

b:103.7
occ:1.00
 F01 C:7N1601 0.0 103.7 1.0
CAL C:7N1601 1.4 104.9 1.0
CAK C:7N1601 2.4 91.3 1.0
CAM C:7N1601 2.4 101.2 1.0
H1 C:7N1601 2.6 109.6 1.0
H2 C:7N1601 2.6 121.5 1.0
CD2 C:LEU100 3.1 94.5 1.0
CD1 C:LEU100 3.6 76.8 1.0
CAJ C:7N1601 3.6 94.4 1.0
CAH C:7N1601 3.7 98.5 1.0
CG C:LEU100 3.9 80.6 1.0
CB C:PRO95 4.1 82.8 1.0
CB C:CYS181 4.1 92.4 1.0
CAI C:7N1601 4.1 98.9 1.0
SG C:CYS181 4.2 129.3 1.0
CH2 C:TRP229 4.2 108.6 1.0
CG C:PRO95 4.4 85.1 1.0
CD2 C:TYR188 4.6 96.1 1.0
CZ3 C:TRP229 4.6 115.1 1.0
CZ2 C:TRP229 4.7 126.8 1.0
CBB C:7N1601 4.8 103.7 1.0
O0A C:7N1601 4.8 98.0 1.0
H5 C:7N1601 4.9 124.5 1.0
CG C:TYR188 4.9 89.5 1.0
C04 C:7N1601 4.9 92.3 1.0
CB C:TYR188 5.0 89.8 1.0

Fluorine binding site 2 out of 4 in 8sts

Go back to Fluorine Binding Sites List in 8sts
Fluorine binding site 2 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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, V106A) 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
C:F601

b:99.7
occ:1.00
 F02 C:7N1601 0.0 99.7 1.0
C01 C:7N1601 1.4 88.9 1.0
C00 C:7N1601 2.4 90.7 1.0
C02 C:7N1601 2.4 89.7 1.0
H7 C:7N1601 2.6 108.9 1.0
H14 C:7N1601 2.6 107.6 1.0
CG1 C:VAL179 2.9 112.8 1.0
CE C:LYS103 3.7 88.2 1.0
C03 C:7N1601 3.7 94.5 1.0
C05 C:7N1601 3.7 97.2 1.0
CG2 C:VAL179 3.7 125.3 1.0
CG C:LYS103 3.8 101.9 1.0
CB C:VAL179 3.9 92.3 1.0
C04 C:7N1601 4.2 92.3 1.0
CD C:LYS103 4.4 89.5 1.0
O C:LYS101 4.4 102.1 1.0
H15 C:7N1601 4.5 113.4 1.0
H9 C:7N1601 4.6 128.6 1.0
H8 C:7N1601 4.7 128.6 1.0
O0B C:7N1601 4.8 109.3 1.0
NZ C:LYS103 4.8 87.8 1.0
H2 C:7N1601 4.9 121.5 1.0
O C:VAL179 4.9 98.3 1.0
SG C:CYS181 4.9 129.3 1.0
C0D C:7N1601 5.0 107.1 1.0
CA C:GLY190 5.0 92.6 1.0

Fluorine binding site 3 out of 4 in 8sts

Go back to Fluorine Binding Sites List in 8sts
Fluorine binding site 3 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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 3 of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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:135.0
occ:1.00
 F01 A:7N1601 0.0 135.0 1.0
CAL A:7N1601 1.4 124.3 1.0
CAK A:7N1601 2.4 120.5 1.0
CAM A:7N1601 2.4 122.5 1.0
H2 A:7N1601 2.6 147.0 1.0
H1 A:7N1601 2.6 144.7 1.0
CD2 A:LEU100 3.3 88.1 1.0
CAH A:7N1601 3.7 113.1 1.0
CAJ A:7N1601 3.7 123.6 1.0
CG A:PRO95 3.9 110.7 1.0
CB A:PRO95 3.9 94.1 1.0
CAI A:7N1601 4.1 114.0 1.0
CH2 A:TRP229 4.1 166.7 1.0
CD1 A:LEU100 4.2 97.7 1.0
SG A:CYS181 4.3 134.8 1.0
CB A:CYS181 4.3 115.2 1.0
CG A:LEU100 4.4 94.1 1.0
CZ3 A:TRP229 4.4 162.0 1.0
CD2 A:TYR188 4.5 114.8 1.0
CBB A:7N1601 4.8 132.0 1.0
O0A A:7N1601 4.8 119.1 1.0
CZ2 A:TRP229 4.9 157.3 1.0
CG B:GLU138 4.9 107.8 1.0
C04 A:7N1601 4.9 121.6 1.0
H5 A:7N1601 4.9 158.4 1.0

Fluorine binding site 4 out of 4 in 8sts

Go back to Fluorine Binding Sites List in 8sts
Fluorine binding site 4 out of 4 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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 4 of Crystal Structure of Hiv-1 Reverse Transcriptase (Y181C, V106A) 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:117.5
occ:1.00
 F02 A:7N1601 0.0 117.5 1.0
C01 A:7N1601 1.4 126.6 1.0
C00 A:7N1601 2.4 119.2 1.0
C02 A:7N1601 2.4 133.8 1.0
H7 A:7N1601 2.6 143.1 1.0
H14 A:7N1601 2.6 160.6 1.0
CB A:VAL179 3.1 119.1 1.0
CG1 A:VAL179 3.3 111.0 1.0
C05 A:7N1601 3.7 130.1 1.0
C03 A:7N1601 3.7 130.0 1.0
CG A:LYS103 3.7 130.6 1.0
O A:VAL179 3.8 117.8 1.0
CG2 A:VAL179 3.9 108.7 1.0
C04 A:7N1601 4.2 121.6 1.0
CD A:LYS103 4.2 125.3 1.0
C A:VAL179 4.2 111.9 1.0
CA A:VAL179 4.2 114.8 1.0
O A:GLY190 4.3 108.3 1.0
N A:GLY190 4.4 101.9 1.0
CA A:GLY190 4.5 110.0 1.0
H15 A:7N1601 4.5 156.1 1.0
H8 A:7N1601 4.6 149.7 1.0
C A:GLY190 4.7 120.2 1.0
H9 A:7N1601 4.8 149.7 1.0
SG A:CYS181 4.8 134.8 1.0
CE A:LYS103 4.8 115.5 1.0
O0B A:7N1601 4.8 141.2 1.0
CB A:LYS103 4.9 130.2 1.0
N A:VAL179 4.9 111.4 1.0
H2 A:7N1601 5.0 147.0 1.0
C0D A:7N1601 5.0 124.7 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: Sat Aug 3 00:09:12 2024

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