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Chlorine in PDB 4zls: Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand)

Enzymatic activity of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand):
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand), PDB code: 4zls 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 / 1.53
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.740, 86.238, 46.067, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Other elements in 4zls:

The structure of Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) 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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) (pdb code 4zls). 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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand), PDB code: 4zls:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4zls

Go back to Chlorine Binding Sites List in 4zls
Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:19.6
occ:1.00
 ND2 A:ASN88 3.2 14.0 1.0
N A:THR74 3.2 15.1 1.0
CA A:GLY73 3.7 12.1 1.0
CB A:ASN88 3.7 10.8 1.0
OG1 A:THR74 3.8 16.4 1.0
CB A:THR74 3.9 17.9 1.0
C A:GLY73 4.0 14.9 1.0
CG A:ASN88 4.0 14.9 1.0
CA A:THR74 4.1 13.0 1.0
O A:HOH631 4.5 20.7 1.0
O A:ASN88 4.6 14.7 1.0
O A:THR74 4.7 15.0 1.0
CA A:ASN88 4.8 11.5 1.0
C A:THR74 4.9 17.6 1.0
C A:ASN88 4.9 15.9 1.0

Chlorine binding site 2 out of 3 in 4zls

Go back to Chlorine Binding Sites List in 4zls
Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:34.3
occ:1.00
 NE2 A:GLN18 3.3 27.9 1.0
OG A:SER37 3.3 27.1 0.4
N A:SER37 3.4 19.2 1.0
CA A:MET36 3.8 17.4 1.0
CB A:MET36 3.9 16.2 1.0
C A:MET36 4.1 19.6 1.0
CB A:SER37 4.3 23.7 0.4
CD A:GLN18 4.3 28.8 1.0
CB A:SER37 4.4 23.2 0.3
CA A:SER37 4.4 18.5 0.4
CB A:SER37 4.5 23.4 0.3
CA A:SER37 4.5 18.9 0.3
CA A:SER37 4.5 18.9 0.3
OG A:SER37 4.5 22.5 0.3
OE1 A:GLN18 4.5 33.2 1.0
O A:SER37 4.7 21.3 1.0

Chlorine binding site 3 out of 3 in 4zls

Go back to Chlorine Binding Sites List in 4zls
Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-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-096-13A (A Boc-Derivative P2-Ligand, 3,-5-Dimethylbiphenyl P1-Ligand) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:15.5
occ:0.75
 NE1 B:TRP6 3.3 16.0 1.0
O A:HOH627 3.3 16.7 1.0
CZ2 B:TRP6 3.9 14.2 1.0
CE2 B:TRP6 3.9 13.4 1.0
CG2 B:THR4 4.3 21.0 1.0
CD1 B:TRP6 4.5 15.7 1.0
O B:HOH338 4.7 34.4 1.0
CB B:THR4 4.9 15.7 1.0

Reference:

A.K.Ghosh, X.Yu, H.L.Osswald, J.Agniswamy, Y.F.Wang, M.Amano, I.T.Weber, H.Mitsuya. Structure-Based Design of Potent Hiv-1 Protease Inhibitors with Modified P1-Biphenyl Ligands: Synthesis, Biological Evaluation, and Enzyme-Inhibitor X-Ray Structural Studies. J.Med.Chem. V. 58 5334 2015.
ISSN: ISSN 0022-2623
PubMed: 26107245
DOI: 10.1021/ACS.JMEDCHEM.5B00676
Page generated: Fri Jul 26 04:44:33 2024

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