Chlorine in PDB 8fui: Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group, PDB code: 8fui was solved by Y.-F.Wang, A.E.Wong-Sam, 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) 33.40 / 1.25
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.451, 86.136, 46.113, 90, 90, 90
R / Rfree (%) 13.9 / 17.6

Other elements in 8fui:

The structure of Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group (pdb code 8fui). 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-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group, PDB code: 8fui:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8fui

Go back to Chlorine Binding Sites List in 8fui
Chlorine binding site 1 out of 4 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 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-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:13.9
occ:0.80
 O A:HOH308 3.0 28.9 1.0
N A:THR74 3.2 11.9 1.0
ND2 A:ASN88 3.2 11.6 1.0
O A:HOH418 3.3 28.8 0.5
CA A:GLY73 3.8 12.2 1.0
OG1 A:THR74 3.8 15.8 1.0
CB A:ASN88 3.8 10.8 1.0
CB A:THR74 3.9 14.1 1.0
C A:GLY73 4.0 11.5 1.0
CG A:ASN88 4.0 10.6 1.0
CA A:THR74 4.1 11.5 1.0
O A:HOH347 4.2 19.9 1.0
O A:HOH369 4.3 29.6 0.5
O A:ASN88 4.6 11.6 1.0
O A:THR74 4.8 12.2 1.0
OD1 A:ASP30 4.9 20.2 0.7
CA A:ASN88 4.9 10.3 1.0

Chlorine binding site 2 out of 4 in 8fui

Go back to Chlorine Binding Sites List in 8fui
Chlorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 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-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl102

b:19.7
occ:1.00
 O A:HOH348 3.3 14.6 1.0
NE1 B:TRP6 3.3 14.6 1.0
CZ2 B:TRP6 3.8 13.5 1.0
CE2 B:TRP6 3.9 13.3 1.0
CG2 B:THR4 4.2 21.0 1.0
CD1 B:TRP6 4.5 14.5 1.0
O B:HOH250 4.7 27.6 0.5
CB B:THR4 4.8 16.2 1.0

Chlorine binding site 3 out of 4 in 8fui

Go back to Chlorine Binding Sites List in 8fui
Chlorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 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-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl103

b:21.8
occ:0.65
 N B:GLY48 3.2 19.6 1.0
O B:HOH228 3.2 19.3 0.7
N60 A:Y9R201 3.3 16.2 0.7
O B:HOH259 3.3 19.0 0.3
O B:HOH206 3.3 33.2 1.0
CA B:ILE47 3.6 17.2 1.0
C57 A:Y9R201 3.7 14.5 0.7
C B:ILE47 3.9 19.7 1.0
CB B:ILE47 3.9 17.1 1.0
N66 A:Y9R201 4.0 16.9 0.7
C55 A:Y9R201 4.0 15.5 0.7
O B:GLY48 4.1 15.9 1.0
C61 A:Y9R201 4.1 15.5 0.7
CA B:GLY48 4.1 20.8 1.0
C54 A:Y9R201 4.1 13.3 0.7
CG2 B:ILE47 4.2 18.8 1.0
C7 A:Y9R201 4.3 12.9 0.3
O B:MET46 4.4 20.9 1.0
CE2 B:PHE53 4.5 25.7 0.3
C B:GLY48 4.6 14.4 1.0
N B:ILE47 4.8 18.5 1.0
C6 A:Y9R201 4.9 12.1 0.3
C72 A:Y9R201 4.9 25.5 0.7
OD2 B:ASP29 5.0 19.7 1.0

Chlorine binding site 4 out of 4 in 8fui

Go back to Chlorine Binding Sites List in 8fui
Chlorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 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-02519A, with N-(2,5-Dimethylphenyl)- 4-(Pyridin-3-Yl)Pyrimidin-2-Amine As P2-P3 Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl104

b:13.7
occ:0.65
 O B:HOH224 2.9 18.9 1.0
ND2 B:ASN88 3.1 12.6 1.0
N B:THR74 3.2 11.6 1.0
OG1 B:THR74 3.7 15.8 1.0
CA B:GLY73 3.8 12.7 1.0
CB B:THR74 3.8 13.2 1.0
CB B:ASN88 3.9 11.8 1.0
C B:GLY73 4.0 11.6 1.0
CG B:ASN88 4.0 10.4 1.0
CA B:THR74 4.1 12.3 1.0
O B:HOH246 4.1 16.9 1.0
NE2 B:GLN92 4.3 16.4 1.0
O B:ASN88 4.4 14.8 1.0
CD2 B:LEU89 4.5 16.0 1.0
O B:THR74 4.7 12.2 1.0
C B:ASN88 4.8 12.0 1.0
CA B:ASN88 4.8 11.3 1.0
C B:THR74 5.0 10.6 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: Tue Jul 30 09:47:46 2024

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