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Chlorine 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:

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

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 4u8w

Go back to Chlorine Binding Sites List in 4u8w
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl203

b:16.5
occ:1.00
 N A:THR74 3.2 10.9 1.0
ND2 A:ASN88 3.3 11.5 1.0
OG1 A:THR74 3.8 15.9 1.0
CA A:GLY73 3.8 12.0 1.0
CB A:ASN88 3.8 10.0 1.0
CB A:THR74 3.8 13.1 1.0
C A:GLY73 4.0 10.3 1.0
CG A:ASN88 4.0 10.0 1.0
CA A:THR74 4.2 10.6 1.0
O A:HOH335 4.3 19.9 1.0
O A:ASN88 4.6 11.8 1.0
O A:THR74 4.8 11.5 1.0
CA A:ASN88 4.9 9.2 1.0

Chlorine binding site 2 out of 3 in 4u8w

Go back to Chlorine Binding Sites List in 4u8w
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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
B:Cl101

b:19.4
occ:1.00
 O B:HOH206 3.5 27.6 1.0
CB B:PRO44 3.9 15.8 1.0
CH2 B:TRP42 4.0 13.4 1.0
CZ3 B:TRP42 4.1 13.3 1.0
CE B:LYS55 4.1 28.4 0.6
NZ B:LYS55 4.7 20.9 0.6
CA B:PRO44 4.8 12.8 1.0
CD B:LYS55 4.9 26.8 0.6
CG B:LYS55 4.9 27.3 0.5
CG B:PRO44 4.9 16.1 1.0

Chlorine binding site 3 out of 3 in 4u8w

Go back to Chlorine Binding Sites List in 4u8w
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl 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
B:Cl102

b:21.4
occ:1.00
 O B:HOH234 2.8 19.3 1.0
N B:THR74 3.2 10.9 1.0
ND2 B:ASN88 3.2 11.4 1.0
OG1 B:THR74 3.7 15.5 1.0
CB B:THR74 3.8 12.2 1.0
CA B:GLY73 3.8 11.9 1.0
CB B:ASN88 3.9 10.6 1.0
C B:GLY73 4.0 10.8 1.0
CG B:ASN88 4.0 10.7 1.0
CA B:THR74 4.1 10.6 1.0
O B:HOH231 4.1 18.0 1.0
NE2 B:GLN92 4.4 13.8 1.0
O B:ASN88 4.4 13.6 1.0
CD2 B:LEU89 4.5 14.8 1.0
O B:THR74 4.7 11.7 1.0
C B:ASN88 4.8 10.4 1.0
CA B:ASN88 4.9 9.7 1.0
C B:THR74 4.9 10.4 1.0

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: Fri Jul 26 02:08:16 2024

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