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Chlorine in PDB 8f0f: Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group, PDB code: 8f0f 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) 34.72 / 1.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.419, 86.235, 46.075, 90, 90, 90
R / Rfree (%) 13.2 / 16.3

Other elements in 8f0f:

The structure of Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group (pdb code 8f0f). 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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group, PDB code: 8f0f:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8f0f

Go back to Chlorine Binding Sites List in 8f0f
Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' 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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:13.8
occ:0.80
 O A:HOH698 3.0 28.3 0.5
O A:HOH604 3.0 27.9 1.0
N A:THR74 3.2 11.2 1.0
ND2 A:ASN88 3.2 11.1 1.0
OG1 A:THR74 3.7 16.4 1.0
CA A:GLY73 3.8 11.2 1.0
CB A:ASN88 3.8 9.6 1.0
CB A:THR74 3.8 13.8 1.0
C A:GLY73 4.0 10.7 1.0
CG A:ASN88 4.0 10.1 1.0
CA A:THR74 4.1 10.8 1.0
O A:HOH651 4.2 21.3 1.0
O A:ASN88 4.7 10.4 1.0
OD1 A:ASP30 4.8 25.3 0.8
O A:THR74 4.9 11.4 1.0
CA A:ASN88 4.9 9.3 1.0

Chlorine binding site 2 out of 3 in 8f0f

Go back to Chlorine Binding Sites List in 8f0f
Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' 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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:17.3
occ:1.00
 O B:HOH414 3.2 27.3 1.0
O B:HOH411 3.3 28.0 0.5
O A:HOH645 3.3 13.6 1.0
NE1 B:TRP6 3.3 11.8 1.0
CZ2 B:TRP6 3.9 11.1 1.0
CE2 B:TRP6 3.9 10.6 1.0
CG2 B:THR4 4.3 17.5 1.0
CD1 B:TRP6 4.4 12.1 1.0
CB B:THR4 4.9 12.9 1.0
O B:HOH350 4.9 22.2 0.5

Chlorine binding site 3 out of 3 in 8f0f

Go back to Chlorine Binding Sites List in 8f0f
Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' 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-110-19A, A Chloroacetamide Derivative Based on Darunavir As P2' Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:13.4
occ:0.70
 O B:HOH336 2.9 16.2 1.0
ND2 B:ASN88 3.1 9.5 1.0
N B:THR74 3.1 9.9 1.0
O B:HOH357 3.4 32.8 1.0
OG1 B:THR74 3.7 12.9 1.0
CB B:THR74 3.8 10.4 1.0
CA B:GLY73 3.8 10.9 1.0
CB B:ASN88 3.8 9.0 1.0
CG B:ASN88 4.0 8.6 1.0
C B:GLY73 4.0 10.4 1.0
CA B:THR74 4.0 9.6 1.0
O B:HOH353 4.0 14.4 1.0
NE2 B:GLN92 4.4 12.4 1.0
O B:ASN88 4.4 11.0 1.0
CD2 B:LEU89 4.5 12.2 1.0
O B:THR74 4.7 10.2 1.0
O B:HOH420 4.7 24.2 0.5
C B:ASN88 4.7 9.1 1.0
CA B:ASN88 4.8 8.3 1.0
C B:THR74 4.9 8.6 1.0

Reference:

A.K.Ghosh, D.Shahabi, M.Kipfmiller, A.K.Ghosh, M.Johnson, Y.F.Wang, J.Agniswamy, M.Amano, I.T.Weber, H.Mitsuya. Evaluation of Darunavir-Derived Hiv-1 Protease Inhibitors Incorporating P2' Amide-Derivatives: Synthesis, Biological Evaluation and Structural Studies. Bioorg.Med.Chem.Lett. 29168 2023.
ISSN: ESSN 1464-3405
PubMed: 36738797
DOI: 10.1016/J.BMCL.2023.129168
Page generated: Tue Jul 30 09:11:32 2024

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