Chlorine in PDB 6u7p: Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand

The structure of Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand, PDB code: 6u7p 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)	34.69 / 1.13
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.491, 86.097, 46.086, 90.00, 90.00, 90.00
R / Rfree (%)	12.5 / 14.1

The structure of Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand (pdb code 6u7p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand, PDB code: 6u7p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:13.3 occ:0.75 O A:HOH346 3.0 30.0 1.0 N A:THR74 3.2 11.7 1.0 ND2 A:ASN88 3.3 11.0 1.0 CA A:GLY73 3.7 11.6 1.0 OG1 A:THR74 3.8 14.6 1.0 CB A:ASN88 3.8 10.4 1.0 CB A:THR74 3.9 12.7 1.0 C A:GLY73 4.0 10.7 1.0 CG A:ASN88 4.0 10.2 1.0 CA A:THR74 4.1 11.1 1.0 O A:HOH347 4.2 18.4 1.0 O A:ASN88 4.7 10.7 1.0 O A:THR74 4.8 11.1 1.0 CA A:ASN88 4.9 9.3 1.0 OD1 A:ASP30 4.9 55.7 0.7

Chlorine binding site 2 out of 5 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:32.0 occ:0.75 N A:ARG8 3.1 12.4 1.0 CB A:LYS7 3.3 20.2 0.5 CG A:ARG8 3.6 13.9 0.7 CD A:LYS7 3.6 31.7 0.5 CG A:ARG8 3.7 13.6 0.3 CA A:LYS7 3.7 14.8 0.5 CA A:LYS7 3.8 13.9 0.5 CB A:LYS7 3.8 18.4 0.5 CB A:ARG8 3.8 12.5 0.7 CB A:ARG8 3.9 12.0 0.3 C A:LYS7 3.9 12.3 1.0 CD A:ARG8 4.0 18.0 0.7 O A:HOH322 4.1 27.1 1.0 CA A:ARG8 4.1 11.6 0.3 CA A:ARG8 4.1 11.4 0.7 CG A:LYS7 4.3 23.2 0.5 NE A:ARG8 4.4 19.1 0.7 NH2 B:ARG87 4.4 12.9 1.0 CG A:LYS7 4.5 23.6 0.5 CE A:LYS7 4.6 30.0 0.5 CD A:ARG8 4.6 15.1 0.3 CD A:LYS7 4.8 27.3 0.5 CZ A:ARG8 5.0 21.1 0.7

Chlorine binding site 3 out of 5 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl101 b:15.2 occ:0.90 O A:HOH341 3.3 12.9 1.0 NE1 B:TRP6 3.3 11.9 1.0 CZ2 B:TRP6 3.9 12.0 1.0 CE2 B:TRP6 3.9 11.0 1.0 CG2 B:THR4 4.2 17.1 1.0 CD1 B:TRP6 4.5 12.2 1.0 O B:HOH248 4.9 32.1 1.0 CB B:THR4 4.9 13.0 1.0

Chlorine binding site 4 out of 5 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran 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-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl102 b:15.5 occ:0.75 O B:HOH230 2.9 17.6 1.0 O B:HOH296 3.1 26.2 0.5 N B:THR74 3.2 10.2 1.0 ND2 B:ASN88 3.2 10.8 1.0 OG1 B:THR74 3.7 13.9 1.0 CA B:GLY73 3.8 11.2 1.0 CB B:THR74 3.8 11.4 1.0 CB B:ASN88 3.9 10.1 1.0 C B:GLY73 4.0 10.5 1.0 CG B:ASN88 4.0 10.1 1.0 O B:HOH246 4.1 16.1 1.0 CA B:THR74 4.1 10.5 1.0 O B:HOH227 4.3 27.2 0.5 NE2 B:GLN92 4.3 13.2 1.0 O B:ASN88 4.5 12.3 1.0 CD2 B:LEU89 4.6 13.7 1.0 O B:HOH307 4.7 32.3 1.0 O B:THR74 4.7 10.7 1.0 C B:ASN88 4.8 9.8 1.0 CA B:ASN88 4.8 9.9 1.0 C B:THR74 5.0 10.0 1.0 O B:HOH252 5.0 30.2 0.7

Chlorine binding site 5 out of 5 in the Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Hiv-1 Wild Type Protease with Grl-03119A, with Phenyl-Boronic-Acid As P2'-Ligand and with A Hexahydro-4H-Furo-Pyran As the P2-Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl103 b:23.5 occ:0.75 O1 B:GOL105 3.0 25.4 0.5 N B:THR12 3.1 10.4 1.0 C1 B:GOL105 3.6 15.9 0.5 CB B:VAL11 3.7 13.2 1.0 CA B:VAL11 3.8 11.0 1.0 CA B:ALA67 3.8 12.6 1.0 CB B:ALA67 3.9 14.4 1.0 C B:VAL11 4.0 10.0 1.0 CB B:THR12 4.0 12.6 1.0 O B:THR12 4.1 11.5 1.0 CA B:THR12 4.1 10.4 1.0 OG1 B:THR12 4.2 16.6 1.0 CG1 B:VAL11 4.2 15.1 1.0 C B:THR12 4.5 9.8 1.0 N B:ALA67 4.6 11.8 1.0 C B:ALA67 4.8 13.0 1.0 CG2 B:VAL11 4.9 14.9 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