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

Go back to Fluorine Binding Sites List in 8fuj
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

Go back to Fluorine Binding Sites List in 8fuj
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: Thu Jul 27 14:23:14 2023

Last articles

Ca in 3Q3G
Ca in 3Q2W
Ca in 3Q08
Ca in 3Q2L
Ca in 3Q2Q
Ca in 3Q0K
Ca in 3Q2J
Ca in 3Q13
Ca in 3PVX
Ca in 3Q00
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy