Atomistry » Fluorine » PDB 5tvj-5ug2 » 5tw3
Atomistry »
  Fluorine »
    PDB 5tvj-5ug2 »
      5tw3 »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy