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Fluorine in PDB 2ykn: Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)

Enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)

All present enzymatic activity of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti):
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 (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 2ykn was solved by J.Boyer, E.Arnoult, M.Medebielle, J.Guillemont, T.Unge, J.Unge, D.Jochmans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.12
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 119.046, 155.576, 152.764, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 27.9

Other elements in 2ykn:

The structure of Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) (pdb code 2ykn). 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 A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti), PDB code: 2ykn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 2ykn

Go back to Fluorine Binding Sites List in 2ykn
Fluorine binding site 1 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)


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 A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1559

b:46.2
occ:1.00
 F10 A:YKN1559 0.0 46.2 1.0
C9 A:YKN1559 1.3 42.6 1.0
F11 A:YKN1559 2.0 46.4 1.0
C8 A:YKN1559 2.2 35.8 1.0
N7 A:YKN1559 2.5 30.9 1.0
S12 A:YKN1559 2.7 50.5 1.0
N15 A:YKN1559 2.9 37.1 1.0
C13 A:YKN1559 3.2 40.1 1.0
O14 A:YKN1559 3.5 34.8 1.0
CG2 A:VAL106 3.5 35.2 1.0
N A:GLY190 3.6 29.1 1.0
CB A:TYR188 3.7 28.6 1.0
C A:VAL189 3.7 30.0 1.0
N A:VAL189 3.8 28.2 1.0
C6 A:YKN1559 3.9 31.3 1.0
C A:TYR188 3.9 29.3 1.0
CA A:GLY190 3.9 30.8 1.0
C16 A:YKN1559 4.0 39.1 1.0
CB A:VAL106 4.0 36.3 1.0
O A:TYR188 4.1 31.4 1.0
CA A:VAL189 4.2 28.4 1.0
O A:VAL189 4.2 29.6 1.0
C1 A:YKN1559 4.2 30.3 1.0
C17 A:YKN1559 4.3 38.3 1.0
CA A:TYR188 4.4 28.9 1.0
N20 A:YKN1559 4.5 37.3 1.0
O A:VAL179 4.6 28.1 1.0
CG A:TYR188 4.8 26.1 1.0

Fluorine binding site 2 out of 2 in 2ykn

Go back to Fluorine Binding Sites List in 2ykn
Fluorine binding site 2 out of 2 in the Crystal Structure of Hiv-1 Reverse Transcriptase (Rt) in Complex with A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti)


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 A Difluoromethylbenzoxazole (Dfmb) Pyrimidine Thioether Derivative, A Non-Nucleoside Rt Inhibitor (Nnrti) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1559

b:46.4
occ:1.00
 F11 A:YKN1559 0.0 46.4 1.0
C9 A:YKN1559 1.3 42.6 1.0
F10 A:YKN1559 2.0 46.2 1.0
C8 A:YKN1559 2.2 35.8 1.0
S12 A:YKN1559 2.7 50.5 1.0
O14 A:YKN1559 3.0 34.8 1.0
N7 A:YKN1559 3.1 30.9 1.0
O A:TYR188 3.3 31.4 1.0
O A:VAL179 3.3 28.1 1.0
C A:TYR188 3.7 29.3 1.0
N A:TYR181 3.7 24.9 1.0
N A:GLY190 3.8 29.1 1.0
C A:VAL179 3.8 28.5 1.0
CG1 A:VAL179 3.8 29.9 1.0
CB A:TYR188 4.0 28.6 1.0
C1 A:YKN1559 4.0 30.3 1.0
C13 A:YKN1559 4.0 40.1 1.0
CB A:TYR181 4.1 24.2 1.0
CB A:VAL179 4.1 30.6 1.0
N A:VAL189 4.1 28.2 1.0
CA A:ILE180 4.1 27.4 1.0
C A:ILE180 4.1 26.4 1.0
C6 A:YKN1559 4.1 31.3 1.0
CA A:VAL189 4.2 28.4 1.0
N A:ILE180 4.2 28.2 1.0
N15 A:YKN1559 4.2 37.1 1.0
C A:VAL189 4.2 30.0 1.0
O A:HOH2162 4.2 26.5 1.0
CA A:GLY190 4.5 30.8 1.0
CA A:TYR188 4.5 28.9 1.0
CA A:TYR181 4.5 24.9 1.0
CA A:VAL179 4.6 30.4 1.0

Reference:

J.Boyer, E.Arnoult, M.Medebielle, J.Guillemont, J.Unge, D.Jochmans. Difluoromethylbenzoxazole Pyrimidine Thioether Derivatives: A Novel Class of Potent Non-Nucleoside Hiv-1 Reverse Transcriptase Inhibitors. J.Med.Chem. V. 54 7974 2011.
ISSN: ISSN 0022-2623
PubMed: 22017513
DOI: 10.1021/JM200766B
Page generated: Wed Jul 31 16:53:46 2024

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