Fluorine in PDB 8dxg: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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- (Trifluoromethyl)Pyridin-2-Ol at W24 Site, PDB code: 8dxg 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) 38.09 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.623, 73.003, 109.791, 90, 100.56, 90
R / Rfree (%) 20.1 / 22.5

Other elements in 8dxg:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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- (Trifluoromethyl)Pyridin-2-Ol at W24 Site (pdb code 8dxg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site, PDB code: 8dxg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8dxg

Go back to Fluorine Binding Sites List in 8dxg
Fluorine binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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- (Trifluoromethyl)Pyridin-2-Ol at W24 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:79.5
occ:1.00
 F A:U4D601 0.0 79.5 1.0
C5 A:U4D601 1.3 81.9 1.0
F2 A:U4D601 2.1 84.4 1.0
F1 A:U4D601 2.1 83.8 1.0
C3 A:U4D601 2.4 77.8 1.0
C2 A:U4D601 2.9 75.5 1.0
O A:HOH930 3.4 64.5 1.0
C4 A:U4D601 3.5 74.1 1.0
C1 A:U4D601 4.2 68.6 1.0
NH2 A:ARG78 4.3 81.2 1.0
N A:U4D601 4.6 72.3 1.0
CG1 A:VAL21 4.7 57.6 1.0
CZ2 A:TRP24 4.8 84.1 1.0
C A:U4D601 4.9 69.1 1.0

Fluorine binding site 2 out of 3 in 8dxg

Go back to Fluorine Binding Sites List in 8dxg
Fluorine binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 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- (Trifluoromethyl)Pyridin-2-Ol at W24 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:83.8
occ:1.00
 F1 A:U4D601 0.0 83.8 1.0
C5 A:U4D601 1.3 81.9 1.0
F2 A:U4D601 2.1 84.4 1.0
F A:U4D601 2.1 79.5 1.0
C3 A:U4D601 2.4 77.8 1.0
CZ2 A:TRP24 3.0 84.1 1.0
C2 A:U4D601 3.0 75.5 1.0
C4 A:U4D601 3.4 74.1 1.0
CH2 A:TRP24 3.6 85.5 1.0
CE2 A:TRP24 3.8 80.6 1.0
NE1 A:TRP24 4.2 79.1 1.0
C1 A:U4D601 4.3 68.6 1.0
N A:U4D601 4.6 72.3 1.0
CZ3 A:TRP24 4.8 80.8 1.0
CD2 A:TRP24 4.9 77.6 1.0
C A:U4D601 4.9 69.1 1.0

Fluorine binding site 3 out of 3 in 8dxg

Go back to Fluorine Binding Sites List in 8dxg
Fluorine binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 5- (Trifluoromethyl)Pyridin-2-Ol at W24 Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:84.4
occ:1.00
 F2 A:U4D601 0.0 84.4 1.0
C5 A:U4D601 1.3 81.9 1.0
F A:U4D601 2.1 79.5 1.0
F1 A:U4D601 2.1 83.8 1.0
C3 A:U4D601 2.4 77.8 1.0
C4 A:U4D601 2.8 74.1 1.0
C2 A:U4D601 3.6 75.5 1.0
N A:U4D601 4.1 72.3 1.0
CG1 A:VAL21 4.4 57.6 1.0
CZ2 A:TRP24 4.5 84.1 1.0
NE1 A:TRP24 4.5 79.1 1.0
CE2 A:TRP24 4.7 80.6 1.0
C1 A:U4D601 4.8 68.6 1.0
O A:HOH930 4.8 64.5 1.0
C A:U4D601 4.9 69.1 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: Thu Jul 27 13:57:08 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy