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Fluorine in PDB 4u8w: Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand), PDB code: 4u8w was solved by Y.-F.Wang, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.539, 85.989, 46.210, 90.00, 90.00, 90.00
R / Rfree (%) 15.4 / 18.8

Other elements in 4u8w:

The structure of Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) (pdb code 4u8w). 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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand), PDB code: 4u8w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4u8w

Go back to Fluorine Binding Sites List in 4u8w
Fluorine binding site 1 out of 4 in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)


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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:12.1
occ:0.55
 F39 A:G10201 0.0 12.1 0.6
C30 A:G10201 1.3 12.5 0.6
F40 A:G10201 2.1 14.6 0.6
O B:GLY48 2.2 14.9 0.6
C31 A:G10201 2.4 11.3 0.6
C6 A:G10201 2.4 11.0 0.5
C29 A:G10201 2.4 13.3 0.6
C12 A:G10201 2.6 10.5 0.5
O23 A:G10201 2.8 10.2 0.6
C21 A:G10201 2.8 10.2 0.6
C24 A:G10201 2.8 11.0 0.6
O22 A:G10201 3.0 13.8 0.6
O10 A:G10201 3.0 11.9 0.5
O B:HOH270 3.0 20.9 0.5
C5 A:G10201 3.2 10.7 0.5
C35 A:G10201 3.2 12.5 0.6
C34 A:G10201 3.3 13.4 0.6
O B:GLY48 3.3 13.0 0.5
C7 A:G10201 3.3 10.8 0.5
C B:GLY48 3.4 15.3 0.5
C B:GLY48 3.4 15.2 0.6
S8 A:G10201 3.4 9.5 0.5
N20 A:G10201 3.4 9.9 0.6
C36 A:G10201 3.5 11.9 0.6
N B:GLY49 3.5 13.2 0.5
C33 A:G10201 3.5 11.0 0.6
N11 A:G10201 3.5 10.3 0.5
O28 A:G10201 3.5 12.1 0.6
C27 A:G10201 3.5 11.4 0.6
C13 A:G10201 3.6 11.3 0.5
O B:HOH225 3.6 14.1 0.5
C38 A:G10201 3.6 10.9 0.6
C37 A:G10201 3.6 11.3 0.6
CA B:GLY49 3.6 13.2 0.5
C15 A:G10201 3.7 11.7 0.5
CA B:GLY49 3.7 13.4 0.6
N B:GLY49 4.0 14.5 0.6
CA B:GLY48 4.1 14.9 0.5
C14 A:G10201 4.2 13.7 0.5
C25 A:G10201 4.3 11.1 0.6
C19 A:G10201 4.3 9.1 0.6
O B:HOH271 4.4 16.9 0.6
O26 A:G10201 4.4 12.1 0.6
C4 A:G10201 4.4 10.7 0.5
C B:GLY49 4.5 12.8 0.5
CA B:GLY48 4.5 17.4 0.6
C32 A:G10201 4.6 10.9 0.6
N B:GLY48 4.6 18.4 0.6
C2 A:G10201 4.6 11.1 0.5
N B:GLY48 4.7 17.6 0.5
C16 A:G10201 4.7 9.7 0.5
O B:GLY27 4.8 11.8 1.0
O9 A:G10201 4.9 11.8 0.5

Fluorine binding site 2 out of 4 in 4u8w

Go back to Fluorine Binding Sites List in 4u8w
Fluorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)


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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:9.9
occ:0.45
 F39 A:G10201 0.0 9.9 0.5
C30 A:G10201 1.3 9.6 0.5
F40 A:G10201 2.2 10.8 0.5
C6 A:G10201 2.3 12.3 0.6
C31 A:G10201 2.3 9.3 0.5
C29 A:G10201 2.4 9.9 0.5
O A:GLY48 2.6 12.5 0.5
C12 A:G10201 2.7 11.0 0.6
O23 A:G10201 2.7 8.8 0.5
C24 A:G10201 2.8 9.9 0.5
C21 A:G10201 2.8 7.9 0.5
O10 A:G10201 2.9 13.4 0.6
O22 A:G10201 3.0 14.1 0.5
C5 A:G10201 3.0 12.3 0.6
C7 A:G10201 3.3 11.9 0.6
S8 A:G10201 3.3 10.5 0.6
O A:GLY48 3.3 13.1 0.6
C35 A:G10201 3.3 8.6 0.5
C36 A:G10201 3.4 10.7 0.5
O A:HOH319 3.4 14.2 0.6
O28 A:G10201 3.5 10.0 0.5
N11 A:G10201 3.5 10.2 0.6
N20 A:G10201 3.5 7.6 0.5
C34 A:G10201 3.5 8.7 0.5
C27 A:G10201 3.5 9.2 0.5
C A:GLY48 3.5 15.0 0.6
C37 A:G10201 3.6 10.6 0.5
C33 A:G10201 3.6 9.1 0.5
C13 A:G10201 3.6 11.3 0.6
N A:GLY49 3.7 13.2 0.6
C A:GLY48 3.7 14.6 0.5
C38 A:G10201 3.7 9.7 0.5
C15 A:G10201 3.7 11.6 0.6
CA A:GLY49 3.8 13.8 0.6
CA A:GLY49 3.9 12.1 0.5
C14 A:G10201 4.1 14.9 0.6
C25 A:G10201 4.2 9.5 0.5
N A:GLY49 4.3 13.1 0.5
C4 A:G10201 4.3 12.2 0.6
C19 A:G10201 4.3 8.1 0.5
O26 A:G10201 4.4 9.0 0.5
C A:GLY49 4.4 13.1 0.6
CA A:GLY48 4.5 15.8 0.6
C2 A:G10201 4.5 11.7 0.6
C32 A:G10201 4.6 8.9 0.5
C16 A:G10201 4.7 9.8 0.6
O9 A:G10201 4.8 14.1 0.6
O A:GLY49 4.8 14.3 0.6
CA A:GLY48 4.9 15.3 0.5
N A:GLY48 4.9 15.2 0.5
O A:HOH339 4.9 26.8 1.0
C3 A:G10201 4.9 12.1 0.6
O A:GLY27 5.0 11.6 1.0
O B:HOH224 5.0 12.2 0.5

Fluorine binding site 3 out of 4 in 4u8w

Go back to Fluorine Binding Sites List in 4u8w
Fluorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)


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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:14.6
occ:0.55
 F40 A:G10201 0.0 14.6 0.6
C30 A:G10201 1.3 12.5 0.6
F39 A:G10201 2.1 12.1 0.6
C29 A:G10201 2.3 13.3 0.6
C31 A:G10201 2.4 11.3 0.6
O B:HOH271 2.5 16.9 0.6
O B:GLY48 2.5 14.9 0.6
O28 A:G10201 2.9 12.1 0.6
C27 A:G10201 3.0 11.4 0.6
O B:HOH272 3.1 17.7 0.5
O B:HOH270 3.1 20.9 0.5
C6 A:G10201 3.3 11.0 0.5
CA B:GLY48 3.3 14.9 0.5
C7 A:G10201 3.4 10.8 0.5
C B:GLY48 3.4 15.3 0.5
O B:HOH225 3.4 14.1 0.5
N B:GLY48 3.5 17.6 0.5
O B:GLY48 3.5 13.0 0.5
C B:GLY48 3.6 15.2 0.6
C24 A:G10201 3.7 11.0 0.6
N B:GLY48 3.8 18.4 0.6
N B:GLY49 4.0 13.2 0.5
C34 A:G10201 4.1 13.4 0.6
C35 A:G10201 4.1 12.5 0.6
O23 A:G10201 4.1 10.2 0.6
O B:HOH256 4.1 24.8 0.6
CA B:GLY48 4.2 17.4 0.6
NH2 A:ARG8 4.2 22.3 0.7
O26 A:G10201 4.3 12.1 0.6
C5 A:G10201 4.5 10.7 0.5
C12 A:G10201 4.5 10.5 0.5
C21 A:G10201 4.7 10.2 0.6
C25 A:G10201 4.7 11.1 0.6
C2 A:G10201 4.7 11.1 0.5
OD2 B:ASP29 4.7 19.9 1.0
N B:GLY49 4.7 14.5 0.6
C33 A:G10201 4.7 11.0 0.6
C B:ILE47 4.7 20.4 0.5
O B:HOH250 4.8 23.2 0.5
CA B:GLY49 4.8 13.2 0.5
C36 A:G10201 4.8 11.9 0.6
O10 A:G10201 4.9 11.9 0.5
O22 A:G10201 4.9 13.8 0.6
C B:ILE47 5.0 20.2 0.6
CA B:GLY49 5.0 13.4 0.6

Fluorine binding site 4 out of 4 in 4u8w

Go back to Fluorine Binding Sites List in 4u8w
Fluorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand)


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-050-10A (A Gem-Difluoro-Bis- Tetrahydrofuran As P2-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:10.8
occ:0.45
 F40 A:G10201 0.0 10.8 0.5
C30 A:G10201 1.3 9.6 0.5
F39 A:G10201 2.2 9.9 0.5
C29 A:G10201 2.3 9.9 0.5
C31 A:G10201 2.3 9.3 0.5
O A:GLY48 2.8 12.5 0.5
C27 A:G10201 3.0 9.2 0.5
O A:HOH339 3.0 26.8 1.0
O28 A:G10201 3.1 10.0 0.5
C6 A:G10201 3.2 12.3 0.6
O A:HOH319 3.3 14.2 0.6
C7 A:G10201 3.4 11.9 0.6
O A:GLY48 3.7 13.1 0.6
C24 A:G10201 3.7 9.9 0.5
C A:GLY48 3.7 15.0 0.6
O A:HOH363 3.9 31.3 0.6
CA A:GLY48 4.0 15.8 0.6
C A:GLY48 4.0 14.6 0.5
O23 A:G10201 4.1 8.8 0.5
N A:GLY48 4.2 15.3 0.6
C35 A:G10201 4.2 8.6 0.5
NH2 B:ARG8 4.2 27.2 0.6
N A:GLY49 4.2 13.2 0.6
N A:GLY48 4.3 15.2 0.5
C34 A:G10201 4.3 8.7 0.5
O26 A:G10201 4.4 9.0 0.5
C5 A:G10201 4.5 12.3 0.6
C12 A:G10201 4.7 11.0 0.6
C25 A:G10201 4.7 9.5 0.5
C2 A:G10201 4.7 11.7 0.6
CA A:GLY48 4.7 15.3 0.5
C21 A:G10201 4.7 7.9 0.5
C36 A:G10201 4.8 10.7 0.5
OD2 A:ASP29 4.8 18.1 1.0
C33 A:G10201 4.9 9.1 0.5
NH2 B:ARG8 4.9 23.9 0.5
O10 A:G10201 4.9 13.4 0.6
N A:GLY49 5.0 13.1 0.5
O22 A:G10201 5.0 14.1 0.5

Reference:

A.K.Ghosh, S.Yashchuk, A.Mizuno, N.Chakraborty, J.Agniswamy, Y.F.Wang, M.Aoki, P.M.Gomez, M.Amano, I.T.Weber, H.Mitsuya. Design of Gem-Difluoro-Bis-Tetrahydrofuran As P2 Ligand For Hiv-1 Protease Inhibitors to Improve Brain Penetration: Synthesis, X-Ray Studies, and Biological Evaluation. Chemmedchem 2014.
ISSN: ESSN 1860-7187
PubMed: 25336073
DOI: 10.1002/CMDC.201402358
Page generated: Sun Dec 13 12:13:05 2020

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