Bromine in PDB 8dx2: Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites

Enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites

All present enzymatic activity of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine 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 4-Amino-3- Bromopyridine at Multiple Sites, PDB code: 8dx2 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) 38.05 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.918, 73.261, 109.247, 90, 100.38, 90
R / Rfree (%) 18.8 / 24.3

Other elements in 8dx2:

The structure of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites (pdb code 8dx2). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites, PDB code: 8dx2:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in 8dx2

Go back to Bromine Binding Sites List in 8dx2
Bromine binding site 1 out of 5 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br608

b:81.2
occ:0.83
 BR04 A:V06608 0.0 81.2 0.8
C03 A:V06608 1.9 80.4 0.8
C02 A:V06608 2.8 75.3 0.8
C05 A:V06608 2.8 81.6 0.8
N01 A:V06608 3.1 75.5 0.8
CG2 A:THR362 3.6 37.2 1.0
O A:LYS512 3.6 43.1 1.0
C A:SER513 3.7 48.1 1.0
CA A:SER513 3.8 46.9 1.0
O A:ALA360 3.8 66.8 1.0
C A:LYS512 3.9 46.3 1.0
N A:SER513 3.9 44.3 1.0
N A:GLU514 4.0 51.0 1.0
N06 A:V06608 4.1 78.3 0.8
C08 A:V06608 4.1 72.5 0.8
O A:SER513 4.2 45.8 1.0
NH1 A:ARG356 4.3 54.2 1.0
O A:GLY359 4.3 87.0 1.0
C A:ALA360 4.4 65.4 1.0
CB A:THR362 4.4 38.3 1.0
N A:THR362 4.5 43.0 1.0
CB A:LYS512 4.5 61.8 1.0
CG A:LYS512 4.5 73.2 1.0
C07 A:V06608 4.6 73.5 0.8
O A:HOH731 4.6 65.8 1.0
CA A:HIS361 4.6 55.1 1.0
CZ A:ARG356 4.7 58.6 1.0
C A:HIS361 4.8 51.6 1.0
N A:HIS361 4.8 50.4 1.0
CA A:GLU514 4.8 57.9 1.0
CA A:LYS512 4.8 49.1 1.0
CG A:GLU514 4.9 75.4 1.0
CD A:ARG356 5.0 51.9 1.0

Bromine binding site 2 out of 5 in 8dx2

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Bromine binding site 2 out of 5 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br609

b:77.1
occ:0.76
 BR04 A:V06609 0.0 77.1 0.8
BR04 A:V06609 0.1 71.2 0.2
C03 A:V06609 1.8 65.2 0.2
C03 A:V06609 1.9 63.6 0.8
O A:HOH870 2.6 73.1 1.0
C05 A:V06609 2.7 64.5 0.2
C02 A:V06609 2.8 60.6 0.2
C05 A:V06609 2.8 56.9 0.8
C02 A:V06609 2.8 63.5 0.8
N01 A:V06609 3.1 65.8 0.8
N01 A:V06609 3.1 58.8 0.2
O A:HOH845 3.7 47.9 1.0
O A:HOH772 4.0 49.4 1.0
N06 A:V06609 4.0 64.0 0.2
N06 A:V06609 4.0 57.9 0.8
C08 A:V06609 4.1 60.6 0.2
C08 A:V06609 4.1 61.5 0.8
CD B:PRO140 4.1 49.6 1.0
CB A:LEU168 4.1 28.8 1.0
CD1 A:LEU168 4.2 44.6 1.0
OG1 A:THR165 4.2 39.1 1.0
CG B:PRO140 4.4 49.6 1.0
CA A:THR165 4.4 43.2 1.0
C07 A:V06609 4.5 61.7 0.2
C07 A:V06609 4.5 62.3 0.8
O A:ILE180 4.7 44.9 1.0
CB A:THR165 4.7 37.0 1.0
CG2 A:THR165 4.8 41.0 1.0
CG A:LEU168 4.9 34.9 1.0
O A:THR165 5.0 37.0 1.0

Bromine binding site 3 out of 5 in 8dx2

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Bromine binding site 3 out of 5 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br609

b:71.2
occ:0.24
 BR04 A:V06609 0.0 71.2 0.2
BR04 A:V06609 0.1 77.1 0.8
C03 A:V06609 1.9 65.2 0.2
C03 A:V06609 1.9 63.6 0.8
O A:HOH870 2.5 73.1 1.0
C05 A:V06609 2.8 64.5 0.2
C05 A:V06609 2.8 56.9 0.8
C02 A:V06609 2.8 60.6 0.2
C02 A:V06609 2.9 63.5 0.8
N01 A:V06609 3.1 58.8 0.2
N01 A:V06609 3.1 65.8 0.8
O A:HOH845 3.7 47.9 1.0
O A:HOH772 4.0 49.4 1.0
N06 A:V06609 4.1 64.0 0.2
N06 A:V06609 4.1 57.9 0.8
C08 A:V06609 4.1 60.6 0.2
CD B:PRO140 4.1 49.6 1.0
CB A:LEU168 4.1 28.8 1.0
C08 A:V06609 4.1 61.5 0.8
CD1 A:LEU168 4.2 44.6 1.0
OG1 A:THR165 4.2 39.1 1.0
CG B:PRO140 4.4 49.6 1.0
CA A:THR165 4.4 43.2 1.0
C07 A:V06609 4.5 61.7 0.2
C07 A:V06609 4.6 62.3 0.8
O A:ILE180 4.7 44.9 1.0
CB A:THR165 4.7 37.0 1.0
CG A:LEU168 4.8 34.9 1.0
CG2 A:THR165 4.9 41.0 1.0
O A:THR165 5.0 37.0 1.0

Bromine binding site 4 out of 5 in 8dx2

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Bromine binding site 4 out of 5 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br505

b:107.2
occ:0.70
 BR04 B:V06505 0.0 107.2 0.7
C03 B:V06505 1.9 87.4 0.7
C05 B:V06505 2.8 75.4 0.7
C02 B:V06505 2.8 78.5 0.7
N01 B:V06505 3.1 79.2 0.7
O B:HOH666 3.5 46.8 1.0
CB B:MET230 3.5 47.5 1.0
O B:VAL108 3.6 49.6 1.0
O B:HOH678 3.9 62.6 1.0
N06 B:V06505 4.0 75.6 0.7
C08 B:V06505 4.1 71.4 0.7
N B:ASP110 4.1 45.4 1.0
N B:GLY231 4.2 56.2 1.0
C B:MET230 4.2 55.9 1.0
N B:TYR232 4.3 55.2 1.0
C07 B:V06505 4.5 72.3 0.7
CB B:ASP110 4.5 41.4 1.0
SD B:MET230 4.5 55.8 1.0
CA B:MET230 4.5 55.7 1.0
C B:VAL108 4.5 54.0 1.0
CA B:LEU109 4.5 48.1 1.0
CG B:MET230 4.6 55.5 1.0
CA B:GLY231 4.6 60.4 1.0
C B:LEU109 4.6 51.1 1.0
O B:MET230 4.6 52.4 1.0
CB B:TYR232 4.7 63.6 1.0
C B:GLY231 4.8 64.4 1.0
CA B:ASP110 4.9 39.8 1.0
N01 B:V06506 4.9 35.0 1.0
BR04 B:V06506 5.0 117.7 1.0
O B:PHE227 5.0 45.9 1.0

Bromine binding site 5 out of 5 in 8dx2

Go back to Bromine Binding Sites List in 8dx2
Bromine binding site 5 out of 5 in the Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Hiv-1 Reverse Transcriptase/Rilpivirine with Bound Fragment 4-Amino-3- Bromopyridine at Multiple Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br506

b:117.7
occ:0.99
 BR04 B:V06506 0.0 117.7 1.0
C03 B:V06506 1.9 73.2 1.0
C05 B:V06506 2.8 49.5 1.0
C02 B:V06506 2.8 39.9 1.0
OD2 B:ASP110 3.0 47.4 1.0
N01 B:V06506 3.1 35.0 1.0
CG B:ARG72 3.6 59.1 1.0
CG B:ASP110 3.6 46.0 1.0
CB B:ASP110 3.7 41.4 1.0
CB B:PHE227 3.7 54.7 1.0
NE B:ARG72 3.8 54.5 1.0
O B:HOH678 3.9 62.6 1.0
CG B:PHE227 3.9 44.3 1.0
N06 B:V06506 4.0 46.8 1.0
C08 B:V06506 4.1 43.2 1.0
CD2 B:PHE227 4.1 44.7 1.0
CD B:ARG72 4.2 62.5 1.0
CG2 B:THR409 4.3 37.6 1.0
SD B:MET230 4.5 55.8 1.0
C07 B:V06506 4.5 41.4 1.0
CB B:ARG72 4.5 33.2 1.0
CD1 B:PHE227 4.6 53.6 1.0
OD1 B:ASP110 4.6 44.9 1.0
CZ B:ARG72 4.8 51.6 1.0
CE2 B:PHE227 4.9 38.7 1.0
BR04 B:V06505 5.0 107.2 0.7
NH2 B:ARG72 5.0 42.5 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 11 05:05:21 2024

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