Fluorine in PDB 8dxj: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine 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 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site, PDB code: 8dxj 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) 42.94 / 1.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.243, 72.809, 109.454, 90, 100.51, 90
R / Rfree (%) 18.7 / 20.7

Other elements in 8dxj:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine 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 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site (pdb code 8dxj). 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 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site, PDB code: 8dxj:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8dxj

Go back to Fluorine Binding Sites List in 8dxj
Fluorine binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine 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 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F608

b:51.1
occ:0.34
 F A:U43608 0.0 51.1 0.3
O A:HOH987 1.1 48.5 0.7
C7 A:U43608 1.3 53.3 0.3
O A:HOH1023 1.9 61.5 1.0
F2 A:U43608 2.1 47.0 0.3
F1 A:U43608 2.1 57.6 0.3
C4 A:U43608 2.4 54.4 0.3
C5 A:U43608 2.9 44.6 0.3
CB A:ALA172 3.3 37.5 1.0
O A:HOH880 3.5 42.6 1.0
C3 A:U43608 3.5 48.3 0.3
CB A:ILE180 3.9 37.3 1.0
CG1 A:ILE180 3.9 50.8 1.0
O A:ILE180 4.1 41.7 1.0
C6 A:U43608 4.2 50.4 0.3
CD1 A:ILE180 4.3 46.5 1.0
O A:HOH1005 4.5 51.6 1.0
CB A:LEU168 4.5 35.0 1.0
O A:HOH727 4.6 43.7 0.8
CA A:ILE180 4.7 32.9 1.0
C2 A:U43608 4.7 43.9 0.3
C A:ILE180 4.7 38.2 1.0
N A:ILE180 4.7 32.4 1.0
CA A:ALA172 4.7 35.2 1.0
O A:LEU168 4.8 36.0 1.0
CG2 A:ILE180 4.9 50.2 1.0
C1 A:U43608 5.0 54.8 0.3
C A:LEU168 5.0 44.3 1.0
CG2 B:THR139 5.0 37.2 1.0

Fluorine binding site 2 out of 3 in 8dxj

Go back to Fluorine Binding Sites List in 8dxj
Fluorine binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine 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 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F608

b:57.6
occ:0.34
 F1 A:U43608 0.0 57.6 0.3
C7 A:U43608 1.3 53.3 0.3
O A:HOH987 1.8 48.5 0.7
F A:U43608 2.1 51.1 0.3
F2 A:U43608 2.1 47.0 0.3
O A:HOH1023 2.2 61.5 1.0
C4 A:U43608 2.4 54.4 0.3
C5 A:U43608 3.1 44.6 0.3
C3 A:U43608 3.3 48.3 0.3
CG2 B:THR139 3.8 37.2 1.0
CB A:ALA172 4.1 37.5 1.0
CB B:THR139 4.2 33.8 1.0
O A:HOH880 4.2 42.6 1.0
O B:HOH746 4.3 64.5 1.0
C6 A:U43608 4.4 50.4 0.3
CD B:PRO140 4.5 40.0 1.0
C2 A:U43608 4.5 43.9 0.3
O A:HOH1005 4.6 51.6 1.0
O A:HOH727 4.8 43.7 0.8
C1 A:U43608 5.0 54.8 0.3

Fluorine binding site 3 out of 3 in 8dxj

Go back to Fluorine Binding Sites List in 8dxj
Fluorine binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine 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 3 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 1-N- Methyl-4-(Trifluoromethyl)Benzene-1,2-Diamine at the Nnrti Adjacent Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F608

b:47.0
occ:0.34
 F2 A:U43608 0.0 47.0 0.3
C7 A:U43608 1.3 53.3 0.3
O A:HOH1023 1.9 61.5 1.0
F A:U43608 2.1 51.1 0.3
F1 A:U43608 2.1 57.6 0.3
C4 A:U43608 2.4 54.4 0.3
C3 A:U43608 2.7 48.3 0.3
O A:HOH987 2.7 48.5 0.7
CA A:GLU169 3.6 48.4 1.0
N A:GLU169 3.6 44.9 1.0
C5 A:U43608 3.6 44.6 0.3
C A:LEU168 3.7 44.3 1.0
CB A:LEU168 3.8 35.0 1.0
CB A:ALA172 3.9 37.5 1.0
O A:LEU168 3.9 36.0 1.0
CG A:GLU169 4.0 58.3 1.0
O A:THR165 4.0 33.1 1.0
C2 A:U43608 4.1 43.9 0.3
CA A:LEU168 4.4 35.3 1.0
CB A:GLU169 4.4 50.1 1.0
CG2 A:THR165 4.6 39.3 1.0
C A:GLU169 4.6 40.1 1.0
O A:GLU169 4.7 42.7 1.0
C6 A:U43608 4.8 50.4 0.3
C A:THR165 4.9 34.5 1.0
CA A:THR165 4.9 33.4 1.0
C1 A:U43608 5.0 54.8 0.3

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

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