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: Fri Aug 2 17:39:54 2024

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