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Fluorine in PDB 2ykm: 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: 2ykm 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 / 2.90
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 / 29

Other elements in 2ykm:

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 2ykm). 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: 2ykm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 2ykm

Go back to Fluorine Binding Sites List in 2ykm
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:49.4
occ:1.00
 F10 A:YKN1559 0.0 49.4 1.0
C9 A:YKN1559 1.3 49.9 1.0
F11 A:YKN1559 2.1 50.9 1.0
C8 A:YKN1559 2.2 47.2 1.0
N7 A:YKN1559 2.5 44.4 1.0
S12 A:YKN1559 2.7 52.8 1.0
N15 A:YKN1559 3.0 50.9 1.0
C13 A:YKN1559 3.3 50.0 1.0
CB A:TYR188 3.4 38.6 1.0
O14 A:YKN1559 3.5 46.0 1.0
C A:TYR188 3.7 38.8 1.0
CG2 A:VAL106 3.7 46.8 1.0
O A:TYR188 3.8 38.3 1.0
N A:GLY190 3.9 43.3 1.0
C6 A:YKN1559 3.9 44.3 1.0
N A:VAL189 3.9 39.6 1.0
C A:VAL189 3.9 42.1 1.0
CA A:GLY190 4.1 46.0 1.0
CA A:TYR188 4.1 38.5 1.0
CB A:VAL106 4.1 47.3 1.0
C16 A:YKN1559 4.2 51.7 1.0
C1 A:YKN1559 4.3 43.9 1.0
O A:VAL189 4.3 42.0 1.0
CA A:VAL189 4.3 40.8 1.0
O A:VAL179 4.5 42.9 1.0
CG A:TYR188 4.6 37.4 1.0
C17 A:YKN1559 4.6 51.6 1.0
N20 A:YKN1559 4.7 50.1 1.0
CG1 A:VAL179 4.9 43.9 1.0

Fluorine binding site 2 out of 2 in 2ykm

Go back to Fluorine Binding Sites List in 2ykm
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:50.9
occ:1.00
 F11 A:YKN1559 0.0 50.9 1.0
C9 A:YKN1559 1.3 49.9 1.0
F10 A:YKN1559 2.1 49.4 1.0
C8 A:YKN1559 2.3 47.2 1.0
S12 A:YKN1559 2.6 52.8 1.0
O14 A:YKN1559 3.0 46.0 1.0
CG1 A:VAL179 3.2 43.9 1.0
N7 A:YKN1559 3.2 44.4 1.0
O A:TYR188 3.4 38.3 1.0
O A:HOH2165 3.5 47.2 1.0
O A:VAL179 3.5 42.9 1.0
N A:TYR181 3.6 37.9 1.0
CB A:TYR181 3.7 36.1 1.0
C A:VAL179 3.9 43.1 1.0
C A:TYR188 3.9 38.8 1.0
C1 A:YKN1559 4.0 43.9 1.0
C13 A:YKN1559 4.0 50.0 1.0
CB A:TYR188 4.1 38.6 1.0
CB A:VAL179 4.1 44.7 1.0
C A:ILE180 4.1 39.1 1.0
C6 A:YKN1559 4.2 44.3 1.0
CA A:TYR181 4.3 36.8 1.0
N A:GLY190 4.3 43.3 1.0
CA A:ILE180 4.3 40.2 1.0
N15 A:YKN1559 4.3 50.9 1.0
N A:ILE180 4.3 41.3 1.0
N A:VAL189 4.5 39.6 1.0
O A:HOH2072 4.6 47.9 1.0
CA A:TYR188 4.7 38.5 1.0
CA A:VAL179 4.7 44.7 1.0
CA A:VAL189 4.7 40.8 1.0
C A:VAL189 4.7 42.1 1.0
CA A:GLY190 4.8 46.0 1.0
O A:ILE180 4.9 38.2 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: Sun Dec 13 11:42:21 2020

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