Fluorine in PDB 8u6r: Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), 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 in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor, PDB code: 8u6r was solved by G.Prucha, S.Henry, 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) 43.48 / 2.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 224.917, 69.98, 106.308, 90, 105.53, 90
R / Rfree (%) 21.5 / 26.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor (pdb code 8u6r). 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 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor, PDB code: 8u6r:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8u6r

Go back to Fluorine Binding Sites List in 8u6r
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), 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 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:111.1
occ:1.00
 F1 A:VP2601 0.0 111.1 1.0
C3 A:VP2601 1.4 109.3 1.0
C2 A:VP2601 2.2 99.4 1.0
F2 A:VP2601 2.4 107.6 1.0
CD2 A:PHE227 3.3 111.9 1.0
CE2 A:PHE227 3.5 112.4 1.0
N1 A:VP2601 3.6 106.5 1.0
O A:LEU234 4.1 112.9 1.0
C A:LEU234 4.3 112.1 1.0
CB A:LEU234 4.3 111.7 1.0
C A:HIS235 4.4 113.2 1.0
N A:PRO236 4.4 113.5 1.0
CB A:VAL106 4.5 102.1 1.0
O A:HIS235 4.5 117.5 1.0
CG1 A:VAL106 4.5 94.8 1.0
CG A:PHE227 4.6 117.7 1.0
C1 A:VP2601 4.6 104.1 1.0
CA A:PRO236 4.6 116.1 1.0
CD A:PRO236 4.6 117.4 1.0
O1 A:VP2601 4.6 104.0 1.0
N A:HIS235 4.7 114.4 1.0
OH A:TYR318 4.7 95.3 1.0
CG2 A:VAL106 4.8 98.6 1.0
CZ A:PHE227 4.9 116.4 1.0
CA A:HIS235 4.9 115.9 1.0
CG A:PRO225 4.9 123.1 1.0
CB A:PRO225 4.9 123.1 1.0
CA A:LEU234 4.9 111.1 1.0
CG A:PRO236 5.0 117.3 1.0

Fluorine binding site 2 out of 2 in 8u6r

Go back to Fluorine Binding Sites List in 8u6r
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase in Complex with 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), 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 3-(2- ((2-Cyanoindolizin-8-Yl)Oxy)Phenoxy)-N-(2,2-Difluoroethyl)Propanamide (JLJ756), A Non-Nucleoside Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:107.6
occ:1.00
 F2 A:VP2601 0.0 107.6 1.0
C3 A:VP2601 1.4 109.3 1.0
C2 A:VP2601 2.3 99.4 1.0
F1 A:VP2601 2.4 111.1 1.0
O1 A:VP2601 2.7 104.0 1.0
N1 A:VP2601 2.9 106.5 1.0
C1 A:VP2601 3.1 104.1 1.0
CA A:PRO236 3.2 116.1 1.0
O A:HIS235 3.3 117.5 1.0
N A:PRO236 3.6 113.5 1.0
C A:HIS235 3.7 113.2 1.0
C A:PRO236 3.8 115.7 1.0
O A:PRO236 3.8 119.1 1.0
OH A:TYR318 3.8 95.3 1.0
CE2 A:TYR318 4.1 95.5 1.0
CB A:PRO236 4.3 111.8 1.0
CZ A:TYR318 4.4 96.0 1.0
CD A:PRO236 4.5 117.4 1.0
C4 A:VP2601 4.6 101.8 1.0
CG A:PRO236 4.6 117.3 1.0
CG2 A:VAL106 4.7 98.6 1.0
N A:ASP237 4.8 105.1 1.0
CA A:HIS235 4.8 115.9 1.0
N A:HIS235 4.9 114.4 1.0

Reference:

G.R.Prucha, S.Henry, K.Hollander, Z.J.Carter, K.A.Spasov, W.L.Jorgensen, K.S.Anderson. Covalent and Noncovalent Strategies For Targeting LYS102 in Hiv-1 Reverse Transcriptase. Eur.J.Med.Chem. V. 262 15894 2023.
ISSN: ISSN 0223-5234
PubMed: 37883896
DOI: 10.1016/J.EJMECH.2023.115894
Page generated: Sat Aug 3 00:48:00 2024

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