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Chlorine in PDB 5bry: Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate), PDB code: 5bry 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 / 1.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.841, 86.325, 45.630, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.5

Other elements in 5bry:

The structure of Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) (pdb code 5bry). 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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate), PDB code: 5bry:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5bry

Go back to Chlorine Binding Sites List in 5bry
Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)


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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:14.5
occ:0.75
 O A:HOH650 3.2 32.9 0.5
N A:THR74 3.2 14.5 1.0
ND2 A:ASN88 3.2 15.2 1.0
CA A:GLY73 3.8 16.4 1.0
OG1 A:THR74 3.8 17.1 1.0
CB A:ASN88 3.8 12.7 1.0
CB A:THR74 3.9 16.8 1.0
C A:GLY73 4.0 14.5 1.0
CG A:ASN88 4.1 14.2 1.0
CA A:THR74 4.2 14.8 1.0
O A:HOH628 4.4 23.7 1.0
O A:ASN88 4.7 13.8 1.0
O A:THR74 4.7 15.4 1.0
CA A:ASN88 4.9 12.0 1.0
O A:HOH647 4.9 22.3 0.4
C A:THR74 5.0 15.0 1.0

Chlorine binding site 2 out of 3 in 5bry

Go back to Chlorine Binding Sites List in 5bry
Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)


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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:40.1
occ:1.00
 N A:SER37 3.1 21.2 1.0
OG A:SER37 3.2 27.0 0.2
NE2 A:GLN18 3.4 41.6 1.0
CA A:MET36 3.7 17.4 1.0
CB A:MET36 3.7 17.1 1.0
C A:MET36 3.9 18.1 1.0
CB A:SER37 4.1 22.9 0.3
CB A:SER37 4.2 23.6 0.2
CA A:SER37 4.2 21.3 0.3
CA A:SER37 4.2 21.2 0.3
CB A:SER37 4.2 23.6 0.3
CA A:SER37 4.2 20.4 0.2
OE1 A:GLN18 4.2 40.0 1.0
CD A:GLN18 4.3 30.8 1.0
O A:SER37 4.4 22.7 1.0
OG A:SER37 4.6 23.4 0.3
C A:SER37 4.8 20.3 1.0
CE A:MET36 5.0 22.2 1.0

Chlorine binding site 3 out of 3 in 5bry

Go back to Chlorine Binding Sites List in 5bry
Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate)


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-011-11A (A Methylamine Bis- Tetrahydrofuran P2-Ligand, Sulfonamide Isostere Derivate) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:16.7
occ:0.75
 O A:HOH626 3.3 17.5 1.0
NE1 B:TRP6 3.3 13.9 1.0
CZ2 B:TRP6 3.8 14.7 1.0
CE2 B:TRP6 3.9 14.0 1.0
CG2 B:THR4 4.2 21.2 1.0
CD1 B:TRP6 4.5 14.1 1.0
CB B:THR4 4.9 16.7 1.0
O B:HOH1031 4.9 27.6 0.5

Reference:

A.K.Ghosh, C.D.Martyr, H.L.Osswald, V.R.Sheri, L.A.Kassekert, S.Chen, J.Agniswamy, Y.F.Wang, H.Hayashi, M.Aoki, I.T.Weber, H.Mitsuya. Design of Hiv-1 Protease Inhibitors with Amino-Bis-Tetrahydrofuran Derivatives As P2-Ligands to Enhance Backbone-Binding Interactions: Synthesis, Biological Evaluation, and Protein-Ligand X-Ray Studies. J.Med.Chem. V. 58 6994 2015.
ISSN: ISSN 0022-2623
PubMed: 26306007
DOI: 10.1021/ACS.JMEDCHEM.5B00900
Page generated: Fri Jul 26 05:39:17 2024

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