Chlorine in PDB 6u7o: Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand

The structure of Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand, PDB code: 6u7o was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.41 / 1.33
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.921, 86.479, 45.875, 90.00, 90.00, 90.00
R / Rfree (%)	13.7 / 17.7

The structure of Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand (pdb code 6u7o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand, PDB code: 6u7o:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:16.9 occ:0.75 O A:HOH696 2.9 31.8 0.5 O A:HOH616 3.0 32.3 1.0 N A:THR74 3.2 13.7 1.0 ND2 A:ASN88 3.2 14.3 1.0 CA A:GLY73 3.7 14.2 1.0 CB A:ASN88 3.8 12.4 1.0 OG1 A:THR74 3.8 18.9 1.0 CB A:THR74 3.9 17.1 1.0 C A:GLY73 4.0 13.4 1.0 CG A:ASN88 4.0 13.5 1.0 CA A:THR74 4.1 13.8 1.0 O A:HOH643 4.2 33.7 0.5 O A:HOH639 4.3 21.9 1.0 O A:ASN88 4.7 13.6 1.0 OD1 A:ASP30 4.8 45.7 0.6 O A:THR74 4.8 13.8 1.0 CA A:ASN88 4.9 12.3 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:30.2 occ:0.75 O A:HOH697 3.0 30.1 0.5 O B:HOH347 3.1 30.6 0.5 N A:ARG8 3.1 13.9 1.0 CB A:LYS7 3.6 23.3 1.0 CG A:ARG8 3.7 14.2 1.0 CA A:LYS7 3.7 15.5 1.0 CB A:ARG8 3.9 13.2 1.0 CG A:LYS7 3.9 34.1 1.0 C A:LYS7 3.9 13.9 1.0 CA A:ARG8 4.1 13.1 1.0 CD A:ARG8 4.1 18.1 1.0 O A:HOH618 4.1 27.5 1.0 NH2 B:ARG87 4.4 14.7 1.0 NE A:ARG8 4.6 20.0 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the 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-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:17.5 occ:0.75 O A:HOH638 3.2 16.7 1.0 NE1 B:TRP6 3.3 15.7 1.0 CZ2 B:TRP6 3.9 15.7 1.0 CE2 B:TRP6 3.9 14.5 1.0 CG2 B:THR4 4.3 21.2 1.0 CD1 B:TRP6 4.5 16.3 1.0 CB B:THR4 4.9 16.7 1.0 O B:HOH322 5.0 27.3 0.7

Chlorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Wild Type Protease with Grl-00819A, with Phenyl-Boronic-Acid As P2'-Ligand and with A 6-5-5-Ring Fused Crown-Like Tetrahydropyranofuran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:18.3 occ:0.75 O B:HOH333 2.9 20.2 1.0 O B:HOH402 3.0 23.1 0.5 ND2 B:ASN88 3.2 13.7 1.0 N B:THR74 3.2 13.7 1.0 CA B:GLY73 3.8 14.4 1.0 OG1 B:THR74 3.8 16.9 1.0 CB B:THR74 3.8 13.7 1.0 CB B:ASN88 3.9 12.9 1.0 C B:GLY73 4.0 13.6 1.0 CG B:ASN88 4.0 12.4 1.0 O B:HOH338 4.1 19.2 1.0 CA B:THR74 4.1 13.6 1.0 NE2 B:GLN92 4.4 16.5 1.0 O B:HOH352 4.4 28.2 0.5 O B:ASN88 4.5 15.1 1.0 CD2 B:LEU89 4.6 16.2 1.0 O B:THR74 4.7 13.8 1.0 C B:ASN88 4.8 11.8 1.0 CA B:ASN88 4.8 12.2 1.0 O B:HOH328 4.9 26.0 0.6 C B:THR74 5.0 12.5 1.0

A.K.Ghosh, Z.Xia, S.Kovela, W.L.Robinson, M.E.Johnson, D.W.Kneller, Y.F.Wang, M.Aoki, Y.Takamatsu, I.T.Weber, H.Mitsuya. Potent Hiv-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-Ray Structural Studies. Chemmedchem V. 14 1863 2019.
ISSN: ESSN 1860-7187
PubMed: 31549492
DOI: 10.1002/CMDC.201900508