Chlorine in PDB 8fuj: Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group, PDB code: 8fuj was solved by Y.-F.Wang, J.Agniswamy, A.K.Ghosh, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.30 / 1.12
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.609, 86.214, 46.189, 90, 90, 90
R / Rfree (%) 12.1 / 13.6

Other elements in 8fuj:

The structure of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group also contains other interesting chemical elements:

Sodium (Na) 1 atom
Fluorine (F) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group (pdb code 8fuj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group, PDB code: 8fuj:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8fuj

Go back to Chlorine Binding Sites List in 8fuj
Chlorine binding site 1 out of 4 in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:10.7
occ:0.75
 O A:HOH626 3.0 25.1 1.0
O A:HOH736 3.1 28.4 0.5
N A:THR74 3.2 7.9 1.0
ND2 A:ASN88 3.2 7.5 1.0
CA A:GLY73 3.8 8.1 1.0
OG1 A:THR74 3.8 10.8 1.0
CB A:ASN88 3.8 6.6 1.0
CB A:THR74 3.8 9.3 1.0
C A:GLY73 4.0 7.5 1.0
CG A:ASN88 4.0 6.3 1.0
CA A:THR74 4.1 7.5 1.0
O A:HOH655 4.1 27.4 0.5
O A:HOH652 4.3 14.6 1.0
O A:ASN88 4.7 7.3 1.0
O A:THR74 4.8 7.7 1.0
CA A:ASN88 4.9 5.7 1.0
OD1 A:ASP30 5.0 15.3 0.6
C A:THR74 5.0 7.0 1.0

Chlorine binding site 2 out of 4 in 8fuj

Go back to Chlorine Binding Sites List in 8fuj
Chlorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:10.3
occ:0.85
 O B:HOH449 3.1 22.0 1.0
O A:HOH656 3.3 8.9 1.0
NE1 B:TRP6 3.3 7.9 1.0
CZ2 B:TRP6 3.9 8.1 1.0
CE2 B:TRP6 3.9 7.4 1.0
CG2 B:THR4 4.2 13.0 1.0
CD1 B:TRP6 4.5 8.0 1.0
CB B:THR4 4.9 9.5 1.0
O B:HOH348 4.9 22.7 0.8

Chlorine binding site 3 out of 4 in 8fuj

Go back to Chlorine Binding Sites List in 8fuj
Chlorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:10.1
occ:0.75
 O B:HOH437 3.0 21.2 0.4
N B:THR74 3.1 5.3 1.0
ND2 B:ASN88 3.2 6.3 1.0
CA B:GLY73 3.7 6.1 1.0
OG1 B:THR74 3.7 8.6 1.0
CB B:ASN88 3.8 6.2 1.0
CB B:THR74 3.8 6.5 1.0
C B:GLY73 3.9 5.2 1.0
CG B:ASN88 4.0 5.3 1.0
CA B:THR74 4.1 5.2 1.0
NE2 B:GLN92 4.3 8.8 1.0
O B:HOH345 4.4 25.4 0.5
O B:ASN88 4.5 7.9 1.0
CD2 B:LEU89 4.6 9.2 1.0
O B:HOH334 4.7 20.5 0.6
O B:THR74 4.7 5.4 1.0
C B:ASN88 4.8 6.0 1.0
CA B:ASN88 4.8 5.6 1.0
C B:THR74 4.9 5.4 1.0

Chlorine binding site 4 out of 4 in 8fuj

Go back to Chlorine Binding Sites List in 8fuj
Chlorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Wild Type Protease with Grl-03419A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group and 3,5- Difluorophenylmethyl As the P1 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:13.6
occ:0.50
 O B:HOH395 0.4 23.9 0.4
O B:HOH453 2.8 26.7 1.0
OG1 B:THR4 2.8 11.0 1.0
O B:HOH446 2.9 26.9 1.0
N B:TRP6 3.3 6.4 1.0
O B:THR4 3.3 9.0 1.0
N B:LYS7 3.4 7.2 1.0
C B:THR4 3.5 7.6 1.0
CB B:TRP6 3.6 7.2 1.0
CG B:LYS7 3.6 12.2 0.5
CA B:TRP6 3.8 6.7 1.0
N B:LEU5 3.9 6.7 1.0
CD1 B:TRP6 3.9 8.0 1.0
O B:HOH316 3.9 12.1 1.0
CB B:THR4 3.9 9.5 1.0
C B:TRP6 4.0 7.0 1.0
C B:LEU5 4.1 6.0 1.0
CG B:TRP6 4.2 7.1 1.0
CB B:LYS7 4.2 11.2 0.5
CG B:LYS7 4.2 14.2 0.5
CA B:THR4 4.2 8.1 1.0
O B:HOH403 4.2 18.6 1.0
CA B:LYS7 4.3 7.8 0.5
CA B:LEU5 4.3 6.0 1.0
O B:HOH348 4.3 22.7 0.8
CA B:LYS7 4.4 7.6 0.5
CB B:LYS7 4.4 10.5 0.5
CE B:LYS7 4.4 32.3 0.5
O B:LYS7 4.5 6.7 1.0
CD B:LYS7 4.5 17.2 0.5
N B:THR4 4.6 8.9 1.0
CE B:LYS7 4.7 17.5 0.5
O B:HOH432 4.8 14.8 1.0
CD B:LYS7 4.8 18.7 0.5
C B:LYS7 4.8 6.5 1.0
O B:HOH416 4.9 31.3 1.0

Reference:

A.K.Ghosh, J.L.Mishevich, S.Kovela, R.Shaktah, A.K.Ghosh, M.Johnson, Y.F.Wang, A.Wong-Sam, J.Agniswamy, M.Amano, Y.Takamatsu, S.I.Hattori, I.T.Weber, H.Mitsuya. Exploration of Imatinib and Nilotinib-Derived Templates As the P2-Ligand For Hiv-1 Protease Inhibitors: Design, Synthesis, Protein X-Ray Structural Studies, and Biological Evaluation. Eur.J.Med.Chem. V. 255 15385 2023.
ISSN: ISSN 0223-5234
PubMed: 37150084
DOI: 10.1016/J.EJMECH.2023.115385
Page generated: Wed Jul 26 16:42:32 2023

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