Fluorine in PDB 8dxi: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites:
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-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites, PDB code: 8dxi 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) 40.32 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.433, 72.831, 109.626, 90, 100.63, 90
R / Rfree (%) 19.1 / 21.8

Other elements in 8dxi:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites 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-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites (pdb code 8dxi). 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 [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites, PDB code: 8dxi:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8dxi

Go back to Fluorine Binding Sites List in 8dxi
Fluorine binding site 1 out of 2 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites


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-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F609

b:59.0
occ:1.00
 F12 A:FMQ609 0.0 59.0 1.0
C9 A:FMQ609 1.4 55.1 1.0
C10 A:FMQ609 2.3 50.9 1.0
C8 A:FMQ609 2.3 54.4 1.0
CA A:MET230 3.5 32.6 1.0
C A:MET230 3.6 36.5 1.0
C11 A:FMQ609 3.6 49.5 1.0
C7 A:FMQ609 3.6 56.4 1.0
O A:MET230 3.9 34.4 1.0
CE A:MET230 4.0 38.5 1.0
N A:GLY231 4.0 34.4 1.0
C6 A:FMQ609 4.1 53.5 1.0
O A:HOH948 4.2 43.6 1.0
CB A:MET230 4.3 35.8 1.0
SD A:MET230 4.3 50.4 1.0
CA A:GLY231 4.7 37.3 1.0
N A:MET230 4.7 35.7 1.0
CG A:MET230 5.0 37.6 1.0
O A:HOH925 5.0 41.5 1.0

Fluorine binding site 2 out of 2 in 8dxi

Go back to Fluorine Binding Sites List in 8dxi
Fluorine binding site 2 out of 2 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment [1-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites


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-(4- Fluorophenyl)-5-Methyl-1H-Pyrazol-4-Yl]Methanol at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:35.9
occ:1.00
 F12 B:FMQ505 0.0 35.9 1.0
C9 B:FMQ505 1.4 32.1 1.0
C8 B:FMQ505 2.3 30.1 1.0
C10 B:FMQ505 2.3 32.8 1.0
CG1 A:ILE380 3.4 19.6 1.0
O B:DMS501 3.4 40.6 1.0
C7 B:FMQ505 3.6 33.3 1.0
C11 B:FMQ505 3.6 33.6 1.0
CA A:THR377 3.7 19.7 1.0
OG1 A:THR377 3.8 25.1 1.0
CB A:ILE380 3.9 20.3 1.0
C1 B:DMS501 4.0 41.9 1.0
C6 B:FMQ505 4.1 29.8 1.0
CB A:THR377 4.2 22.0 1.0
CG2 B:THR400 4.3 21.8 1.0
CG2 A:THR377 4.3 27.3 1.0
CG2 A:ILE380 4.3 20.0 1.0
O B:THR400 4.3 26.3 1.0
N A:THR377 4.4 17.0 1.0
CB B:PRO25 4.4 23.7 1.0
S B:DMS501 4.5 50.9 1.0
O A:THR376 4.5 20.1 1.0
CA B:THR400 4.6 22.4 1.0
O A:THR377 4.6 22.8 1.0
CG B:PRO25 4.6 24.7 1.0
CD1 A:ILE380 4.7 21.6 1.0
C A:THR376 4.7 19.6 1.0
CG2 A:THR376 4.7 17.1 1.0
C A:THR377 4.7 22.8 1.0
O B:PRO25 4.7 20.4 1.0
CB B:THR400 4.9 23.6 1.0
C B:THR400 5.0 25.3 1.0
CD B:PRO25 5.0 23.8 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: Fri Aug 2 17:39:53 2024

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