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Fluorine in PDB 8dxb: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid 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 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site, PDB code: 8dxb 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) 36.56 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.618, 73.128, 109.24, 90, 100.62, 90
R / Rfree (%) 21.3 / 23.5

Other elements in 8dxb:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid 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 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site (pdb code 8dxb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site, PDB code: 8dxb:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8dxb

Go back to Fluorine Binding Sites List in 8dxb
Fluorine binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid 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 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:85.5
occ:1.00
 F14 A:FIC901 0.0 85.5 1.0
C5 A:FIC901 1.4 65.3 1.0
C4 A:FIC901 2.3 64.3 1.0
C6 A:FIC901 2.3 61.2 1.0
CG A:GLU169 2.5 66.1 1.0
O A:THR165 3.0 43.5 1.0
CG2 A:THR165 3.0 49.9 1.0
CD A:GLU169 3.4 79.5 1.0
OE2 A:GLU169 3.5 74.2 1.0
CB A:GLU169 3.5 57.0 1.0
CA A:GLU169 3.6 59.1 1.0
C9 A:FIC901 3.6 62.5 1.0
C7 A:FIC901 3.6 55.0 1.0
N A:GLU169 3.7 53.3 1.0
C A:THR165 3.7 46.5 1.0
CA A:THR165 3.9 48.3 1.0
CB A:THR165 4.0 47.6 1.0
C8 A:FIC901 4.1 53.1 1.0
C A:LEU168 4.5 54.1 1.0
OE1 A:GLU169 4.5 76.5 1.0
OG1 A:THR165 4.7 46.7 1.0
N A:LYS166 4.8 46.2 1.0
CD B:PRO140 4.8 46.3 1.0
CG B:PRO140 4.9 51.2 1.0
CB A:LEU168 4.9 44.9 1.0
C3 A:FIC901 4.9 58.9 1.0

Fluorine binding site 2 out of 2 in 8dxb

Go back to Fluorine Binding Sites List in 8dxb
Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid 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 2 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- Fluoroindole-2-Carboxylic Acid at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:97.6
occ:0.75
 F14 A:FIC902 0.0 97.6 0.8
C5 A:FIC902 1.4 94.2 0.8
C4 A:FIC902 2.3 92.3 0.8
C6 A:FIC902 2.3 79.4 0.8
OE1 A:GLN428 3.1 64.2 0.2
C9 A:FIC902 3.6 81.4 0.8
C7 A:FIC902 3.6 66.7 0.8
O A:HOH1112 3.8 67.9 1.0
CB A:GLN428 3.8 57.7 0.8
CB A:GLN428 3.8 58.2 0.2
CD A:GLN428 4.0 61.6 0.2
C8 A:FIC902 4.1 78.1 0.8
CG A:GLN428 4.3 59.7 0.2
CG A:GLN428 4.4 59.6 0.8
O A:GLN428 4.5 43.9 0.8
CA A:GLN428 4.8 54.4 0.2
CA A:GLN428 4.8 58.7 0.8
N A:GLN428 4.9 48.8 0.8
C3 A:FIC902 4.9 71.3 0.8

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: Fri Aug 2 17:39:53 2024

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