Fluorine 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:

Chlorine (Cl) 4 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 8fuj

Go back to Fluorine Binding Sites List in 8fuj
Fluorine 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 Fluorine with other atoms in the F 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
B:F201

b:15.1
occ:0.55
 F61 B:Y9N201 0.0 15.1 0.6
C34 B:Y9N201 1.3 10.4 0.6
O B:HOH391 2.3 15.8 0.5
C33 B:Y9N201 2.3 8.9 0.6
C35 B:Y9N201 2.3 8.1 0.6
C15 B:Y9N201 2.7 9.4 0.5
O A:HOH601 2.9 23.5 0.5
O A:HOH710 3.3 13.2 0.6
NH2 A:ARG8 3.4 14.8 0.4
O B:HOH361 3.5 13.4 1.0
C36 B:Y9N201 3.6 6.8 0.6
C12 B:Y9N201 3.6 9.5 0.5
C38 B:Y9N201 3.6 6.6 0.6
C13 B:Y9N201 3.7 10.4 0.5
CZ A:ARG8 3.9 13.8 0.4
C56 B:Y9N201 4.0 9.2 0.6
CG2 A:VAL82 4.0 14.3 0.6
NH1 A:ARG8 4.0 14.6 0.4
O B:HOH371 4.1 11.2 1.0
C37 B:Y9N201 4.1 6.7 0.6
O B:GLY48 4.1 11.2 1.0
C6 B:Y9N201 4.3 8.5 0.5
CG1 A:VAL82 4.4 16.6 0.5
C51 B:Y9N201 4.5 6.6 0.6
C14 B:Y9N201 4.5 13.6 0.5
CG2 A:VAL82 4.5 10.3 0.5
N60 B:Y9N201 4.5 10.1 0.6
C55 B:Y9N201 4.6 9.2 0.6
C21 B:Y9N201 4.6 5.5 0.6
O B:GLY27 4.6 8.3 1.0
O A:HOH699 4.7 27.0 0.5
C61 B:Y9N201 4.7 11.7 0.6
F62 B:Y9N201 4.7 8.9 0.6
C7 B:Y9N201 4.7 6.7 0.5
N62 B:Y9N201 4.8 13.3 0.6
O B:HOH433 4.8 25.5 1.0
C32 B:Y9N201 4.9 5.0 0.6
NE A:ARG8 4.9 8.8 0.4
N20 B:Y9N201 4.9 5.4 0.6
O22 B:Y9N201 4.9 9.2 0.6
O B:HOH422 4.9 10.4 0.5
N11 B:Y9N201 5.0 7.2 0.5

Fluorine binding site 2 out of 4 in 8fuj

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Fluorine 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 Fluorine with other atoms in the F 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:F201

b:16.2
occ:0.45
 F61 B:Y9N201 0.0 16.2 0.5
C34 B:Y9N201 1.4 11.8 0.5
O A:HOH645 2.2 21.0 0.6
C35 B:Y9N201 2.3 13.1 0.5
C33 B:Y9N201 2.4 9.7 0.5
C15 B:Y9N201 2.8 8.7 0.6
O B:HOH431 3.2 13.0 0.6
O A:HOH654 3.3 11.3 1.0
O B:HOH429 3.3 19.7 0.5
NH2 B:ARG8 3.4 12.4 0.4
C12 B:Y9N201 3.4 6.3 0.6
C36 B:Y9N201 3.6 11.0 0.5
C38 B:Y9N201 3.7 8.0 0.5
O B:HOH460 3.7 26.9 1.0
C13 B:Y9N201 3.8 7.2 0.6
O A:HOH631 3.9 12.0 1.0
CZ B:ARG8 3.9 10.8 0.4
NH1 B:ARG8 4.1 11.8 0.4
C56 B:Y9N201 4.1 6.2 0.5
C37 B:Y9N201 4.1 8.1 0.5
CG2 B:VAL82 4.2 14.5 0.5
O A:GLY48 4.3 8.6 1.0
O B:HOH394 4.3 24.9 0.5
C6 B:Y9N201 4.4 7.2 0.6
O A:GLY27 4.5 7.5 1.0
N62 B:Y9N201 4.6 8.7 0.5
C51 B:Y9N201 4.6 6.1 0.5
C21 B:Y9N201 4.6 7.4 0.5
C55 B:Y9N201 4.7 6.0 0.5
C7 B:Y9N201 4.7 6.1 0.6
CG2 B:VAL82 4.7 19.3 0.6
F62 B:Y9N201 4.7 14.0 0.5
N60 B:Y9N201 4.7 6.9 0.5
C14 B:Y9N201 4.7 7.8 0.6
C61 B:Y9N201 4.8 7.3 0.5
N11 B:Y9N201 4.9 5.9 0.6
C32 B:Y9N201 4.9 7.4 0.5
N20 B:Y9N201 4.9 6.8 0.5
NE B:ARG8 4.9 9.0 0.4
O22 B:Y9N201 5.0 11.5 0.5

Fluorine binding site 3 out of 4 in 8fuj

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Fluorine 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 Fluorine with other atoms in the F 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:F201

b:8.9
occ:0.55
 F62 B:Y9N201 0.0 8.9 0.6
C36 B:Y9N201 1.4 6.8 0.6
C37 B:Y9N201 2.3 6.7 0.6
C35 B:Y9N201 2.3 8.1 0.6
CG A:PRO81 2.4 14.4 0.5
N B:ILE50 2.8 9.9 0.3
CD A:PRO81 2.8 11.8 0.5
C B:GLY49 3.0 9.7 1.0
C14 B:Y9N201 3.1 13.6 0.5
N B:ILE50 3.2 10.1 0.7
CA B:ILE50 3.2 9.8 0.7
CG A:PRO81 3.3 12.3 0.6
O B:GLY49 3.3 11.0 1.0
O B:HOH391 3.3 15.8 0.5
CD A:PRO81 3.3 11.9 0.6
CB A:PRO81 3.4 11.1 0.6
CA B:ILE50 3.5 8.5 0.3
C34 B:Y9N201 3.6 10.4 0.6
C38 B:Y9N201 3.6 6.6 0.6
CA B:GLY49 3.7 13.2 1.0
CG1 B:ILE50 3.7 10.9 0.3
CB A:PRO81 3.9 12.7 0.5
CB B:ILE50 4.0 10.0 0.7
C33 B:Y9N201 4.1 8.9 0.6
C13 B:Y9N201 4.1 10.4 0.5
C15 B:Y9N201 4.1 9.4 0.5
CB B:ILE50 4.1 10.2 0.3
N A:PRO81 4.2 10.2 1.0
CG2 A:VAL82 4.3 10.3 0.5
CG1 B:ILE50 4.4 13.2 0.7
CA A:PRO81 4.4 11.5 0.6
C B:ILE50 4.5 7.5 0.7
OG1 A:THR80 4.5 8.6 1.0
O22 B:Y9N201 4.5 9.2 0.6
O B:GLY48 4.6 11.2 1.0
CA A:PRO81 4.6 10.8 0.5
N B:GLY49 4.6 12.5 1.0
F61 B:Y9N201 4.7 15.1 0.6
N A:VAL82 4.7 8.9 1.0
O B:HOH433 4.7 25.5 1.0
O B:HOH320 4.7 19.5 1.0
O B:HOH312 4.7 8.8 1.0
CG2 A:VAL82 4.8 14.3 0.6
C12 B:Y9N201 4.8 9.5 0.5
C B:ILE50 4.8 8.3 0.3
O B:ILE50 4.9 9.4 0.7
C32 B:Y9N201 4.9 5.0 0.6
CD1 B:ILE50 4.9 11.1 0.3
O10 B:Y9N201 4.9 8.3 0.5
O9 B:Y9N201 4.9 6.1 0.6
C B:GLY48 4.9 10.4 1.0
C A:PRO81 4.9 10.6 1.0

Fluorine binding site 4 out of 4 in 8fuj

Go back to Fluorine Binding Sites List in 8fuj
Fluorine 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 Fluorine with other atoms in the F 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:F201

b:14.0
occ:0.45
 F62 B:Y9N201 0.0 14.0 0.5
C36 B:Y9N201 1.4 11.0 0.5
CG B:PRO81 1.7 13.9 0.6
C35 B:Y9N201 2.3 13.1 0.5
C37 B:Y9N201 2.4 8.1 0.5
CD B:PRO81 2.5 13.9 0.6
CA A:GLY49 2.9 12.2 1.0
CD B:PRO81 2.9 13.5 0.5
N A:ILE50 2.9 8.4 0.7
C A:GLY49 3.0 10.2 1.0
C14 B:Y9N201 3.1 7.8 0.6
CG B:PRO81 3.1 15.3 0.5
CB B:PRO81 3.1 13.3 0.6
N A:ILE50 3.3 9.7 0.3
O A:HOH645 3.3 21.0 0.6
CB B:PRO81 3.3 15.2 0.5
C34 B:Y9N201 3.6 11.8 0.5
CA A:ILE50 3.6 11.3 0.3
C38 B:Y9N201 3.6 8.0 0.5
O A:GLY49 3.7 9.8 1.0
C15 B:Y9N201 3.9 8.7 0.6
N B:PRO81 3.9 11.4 1.0
CG1 A:ILE50 4.0 9.2 0.7
C13 B:Y9N201 4.0 7.2 0.6
CA A:ILE50 4.0 7.9 0.7
C33 B:Y9N201 4.1 9.7 0.5
CA B:PRO81 4.1 11.5 0.6
CB A:ILE50 4.2 11.1 0.3
N A:GLY49 4.2 9.9 1.0
CA B:PRO81 4.2 11.8 0.5
OG1 B:THR80 4.5 10.4 1.0
C12 B:Y9N201 4.5 6.3 0.6
O22 B:Y9N201 4.5 11.5 0.5
CB A:ILE50 4.6 8.3 0.7
CG2 B:VAL82 4.6 19.3 0.6
N B:VAL82 4.6 9.9 1.0
CG1 A:ILE50 4.6 16.5 0.3
O A:GLY48 4.6 8.6 1.0
O B:HOH312 4.7 8.8 1.0
F61 B:Y9N201 4.7 16.2 0.5
CG2 B:VAL82 4.7 14.5 0.5
C B:PRO81 4.7 10.7 1.0
C A:ILE50 4.8 9.5 0.3
C A:GLY48 4.8 8.3 1.0
O10 B:Y9N201 4.8 6.7 0.6
C32 B:Y9N201 4.9 7.4 0.5
CB B:VAL82 4.9 14.3 0.5
O9 B:Y9N201 5.0 9.1 0.5
CD1 A:ILE50 5.0 11.1 0.7

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: Fri Aug 2 19:26:00 2024

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