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Chlorine in PDB 3ok9: Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A

Enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A

All present enzymatic activity of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A:
3.4.23.16;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A, PDB code: 3ok9 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) 10.00 / 1.27
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.546, 86.212, 45.635, 90.00, 90.00, 90.00
R / Rfree (%) 14.5 / 18.9

Other elements in 3ok9:

The structure of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A (pdb code 3ok9). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A, PDB code: 3ok9:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3ok9

Go back to Chlorine Binding Sites List in 3ok9
Chlorine binding site 1 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl512

b:20.0
occ:1.00
 O A:HOH1048 3.1 31.2 1.0
NE1 A:TRP6 3.3 14.2 1.0
O B:HOH1033 3.3 15.6 1.0
CZ2 A:TRP6 3.9 13.8 1.0
CE2 A:TRP6 3.9 13.9 1.0
CG2 A:THR4 4.3 20.6 1.0
CD1 A:TRP6 4.4 13.9 1.0
CB A:THR4 4.9 15.7 1.0

Chlorine binding site 2 out of 6 in 3ok9

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Chlorine binding site 2 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl516

b:22.7
occ:1.00
 O A:HOH1016 2.9 19.4 1.0
N A:THR74 3.1 13.3 1.0
ND2 A:ASN88 3.2 14.4 1.0
CA A:GLY73 3.7 13.8 1.0
CB A:THR74 3.8 15.0 1.0
OG1 A:THR74 3.8 18.1 1.0
CB A:ASN88 3.9 13.7 1.0
C A:GLY73 3.9 13.2 1.0
CA A:THR74 4.0 13.5 1.0
CG A:ASN88 4.0 12.9 1.0
O A:HOH1020 4.1 19.5 1.0
NE2 A:GLN92 4.4 15.7 1.0
O A:ASN88 4.4 15.0 1.0
CD2 A:LEU89 4.5 17.3 1.0
O A:THR74 4.7 14.3 1.0
C A:ASN88 4.8 12.2 1.0
CA A:ASN88 4.8 12.6 1.0
C A:THR74 4.9 13.2 1.0

Chlorine binding site 3 out of 6 in 3ok9

Go back to Chlorine Binding Sites List in 3ok9
Chlorine binding site 3 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl511

b:14.4
occ:0.75
 O B:HOH1145 2.9 23.3 0.2
N B:THR174 3.2 13.6 1.0
ND2 B:ASN188 3.3 14.9 1.0
OG1 B:THR174 3.8 17.4 1.0
CA B:GLY173 3.8 13.9 1.0
CB B:ASN188 3.8 11.8 1.0
CB B:THR174 3.9 15.5 1.0
C B:GLY173 4.0 13.7 1.0
CG B:ASN188 4.1 12.5 1.0
CA B:THR174 4.2 13.3 1.0
O B:HOH1035 4.4 23.1 1.0
O B:ASN188 4.7 13.3 1.0
O B:THR174 4.7 14.0 1.0
CA B:ASN188 4.9 11.5 1.0
C B:THR174 5.0 12.8 1.0

Chlorine binding site 4 out of 6 in 3ok9

Go back to Chlorine Binding Sites List in 3ok9
Chlorine binding site 4 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl513

b:26.8
occ:0.65
 O B:HOH1072 3.0 25.8 0.5
OG B:SER137 3.2 41.8 0.7
N B:SER137 3.2 20.0 1.0
OE1 B:GLN118 3.4 38.5 1.0
CA B:MET136 3.7 16.0 1.0
CB B:MET136 3.7 16.1 1.0
C B:MET136 4.0 16.3 1.0
CB B:SER137 4.2 25.5 0.7
CD B:GLN118 4.2 27.4 1.0
CA B:SER137 4.2 20.1 0.7
CB B:SER137 4.2 23.9 0.3
CA B:SER137 4.3 20.9 0.3
NE2 B:GLN118 4.3 34.4 1.0
OG B:SER137 4.4 30.7 0.3
O B:SER137 4.5 22.1 1.0
C B:SER137 4.9 18.8 1.0
CE B:MET136 4.9 22.3 1.0
CG B:MET136 5.0 16.5 1.0

Chlorine binding site 5 out of 6 in 3ok9

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Chlorine binding site 5 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl514

b:37.5
occ:0.75
 N B:GLY148 3.2 16.6 0.5
N B:GLY148 3.2 15.7 0.6
C43 A:G52401 3.5 12.7 0.5
CA B:ILE147 3.7 15.8 1.0
C42 A:G52401 3.9 14.4 0.5
C B:ILE147 4.0 14.7 1.0
C40 A:G52401 4.0 15.9 0.6
CA B:GLY148 4.1 15.7 0.5
CB B:ILE147 4.1 17.1 1.0
O B:GLY148 4.2 20.8 0.6
CA B:GLY148 4.2 18.3 0.6
O B:GLY148 4.3 11.6 0.5
CG2 B:ILE147 4.3 25.0 1.0
CE2 B:PHE153 4.3 17.8 1.0
O B:MET146 4.4 18.3 1.0
C31 A:G52401 4.4 12.0 0.5
O B:HOH1086 4.5 32.8 1.0
C7 A:G52401 4.6 14.1 0.6
C30 A:G52401 4.6 11.0 0.5
C B:GLY148 4.6 13.7 0.5
O A:HOH1139 4.7 32.2 0.5
C B:GLY148 4.7 16.6 0.6
C27 A:G52401 4.8 11.7 0.5
O A:HOH1058 4.8 29.7 1.0
N B:ILE147 4.8 14.4 1.0
CD2 B:PHE153 5.0 16.1 1.0

Chlorine binding site 6 out of 6 in 3ok9

Go back to Chlorine Binding Sites List in 3ok9
Chlorine binding site 6 out of 6 in the Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Wild-Type Hiv-1 Protease with New Oxatricyclic Designed Inhibitor Grl-0519A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl515

b:39.5
occ:0.75
 O B:HOH1175 2.9 37.2 0.5
O B:HOH1095 2.9 30.2 0.5
N B:GLU121 3.3 18.8 1.0
O B:HOH1176 3.4 39.7 0.5
CB B:LYS120 3.5 22.0 0.3
OE2 B:GLU134 3.6 19.6 0.2
ND2 B:ASN183 3.6 19.0 1.0
CA B:LYS120 3.7 20.3 0.3
CA B:LYS120 3.7 20.7 0.7
CB B:LYS120 3.8 22.0 0.7
O B:GLU121 3.9 18.4 1.0
C B:LYS120 4.0 18.5 1.0
CG B:LYS120 4.1 23.6 0.7
CA B:GLU121 4.2 18.4 0.4
CB B:GLU121 4.2 21.9 0.4
CA B:GLU121 4.2 18.5 0.6
CB B:GLU121 4.5 21.4 0.6
CG B:LYS120 4.5 23.7 0.3
C B:GLU121 4.5 18.2 1.0
CD B:GLU134 4.6 25.7 0.2
CD B:LYS120 4.6 24.3 0.3
OE1 B:GLU134 4.7 34.7 0.2
O B:HOH1044 4.8 31.8 1.0
CE B:LYS120 4.8 26.9 0.3
CG B:ASN183 4.9 16.9 1.0
CG B:GLU121 5.0 24.2 0.6

Reference:

A.K.Ghosh, C.X.Xu, K.V.Rao, A.Baldridge, J.Agniswamy, Y.F.Wang, I.T.Weber, M.Aoki, S.G.Miguel, M.Amano, H.Mitsuya. Probing Multidrug-Resistance and Protein-Ligand Interactions with Oxatricyclic Designed Ligands in Hiv-1 Protease Inhibitors. Chemmedchem V. 5 1850 2010.
ISSN: ISSN 1860-7179
PubMed: 20827746
DOI: 10.1002/CMDC.201000318
Page generated: Fri Jul 11 08:45:09 2025

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