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Fluorine in PDB 8dxe: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

Protein crystallography data

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site, PDB code: 8dxe was solved by A.Chopra, F.X.Ruiz, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.06 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.226, 72.717, 109.555, 90, 100.51, 90
R / Rfree (%) 18.9 / 21.7

Other elements in 8dxe:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site (pdb code 8dxe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site, PDB code: 8dxe:

Fluorine binding site 1 out of 1 in 8dxe

Go back to Fluorine Binding Sites List in 8dxe
Fluorine binding site 1 out of 1 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 2-Amino-6- Fluorobenzonitrile at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:46.7
occ:0.59
 F07 A:0IF601 0.0 46.7 0.6
C06 A:0IF601 1.4 44.3 0.6
C05 A:0IF601 2.3 46.1 0.6
C08 A:0IF601 2.3 40.0 0.6
CA A:THR165 2.7 32.4 1.0
C09 A:0IF601 2.8 44.0 0.6
OG1 A:THR165 2.9 34.6 1.0
CB A:THR165 3.1 35.5 1.0
CG2 A:THR165 3.3 39.8 1.0
O A:THR165 3.3 30.7 1.0
N10 A:0IF601 3.5 47.1 0.6
O A:HOH999 3.5 54.2 1.0
C A:THR165 3.5 29.0 1.0
C04 A:0IF601 3.6 48.2 0.6
C02 A:0IF601 3.6 38.6 0.6
CB A:LEU168 3.7 33.4 1.0
N A:THR165 3.8 30.4 1.0
CD1 A:LEU168 4.0 35.2 1.0
C03 A:0IF601 4.1 44.3 0.6
O A:MET164 4.2 32.5 1.0
C A:MET164 4.3 28.1 1.0
CG A:LEU168 4.4 33.5 1.0
CG B:PRO140 4.5 36.1 1.0
N A:GLU169 4.6 40.2 1.0
CD B:PRO140 4.7 35.9 1.0
CA A:LEU168 4.7 36.8 1.0
N01 A:0IF601 4.8 42.9 0.6
N A:LYS166 4.8 30.1 1.0
C A:LEU168 4.9 39.4 1.0
N A:LEU168 4.9 34.6 1.0
O A:HOH996 5.0 37.8 1.0

Reference:

A.Chopra, J.D.Bauman, F.X.Ruiz, E.Arnold. Halo Library, A Tool For Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening. J.Med.Chem. V. 66 6013 2023.
ISSN: ISSN 0022-2623
PubMed: 37115705
DOI: 10.1021/ACS.JMEDCHEM.2C01681
Page generated: Wed Jul 16 03:30:20 2025

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