Chlorine in PDB 6e7j: Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand, PDB code: 6e7j 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)	49.10 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.793, 86.043, 45.875, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 18.2

The structure of Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand (pdb code 6e7j). 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand, PDB code: 6e7j:
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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:17.0 occ:0.80 O A:HOH364 3.0 28.1 1.0 N A:THR74 3.2 13.5 1.0 ND2 A:ASN88 3.3 14.9 1.0 CA A:GLY73 3.8 15.1 1.0 CB A:ASN88 3.8 13.5 1.0 OG1 A:THR74 3.9 17.1 1.0 CB A:THR74 3.9 16.2 1.0 C A:GLY73 4.0 15.4 1.0 CG A:ASN88 4.0 13.8 1.0 CA A:THR74 4.2 13.7 1.0 O A:HOH334 4.4 21.2 1.0 O A:ASN88 4.6 14.1 1.0 O A:THR74 4.7 14.4 1.0 CA A:ASN88 4.8 12.1 1.0 O A:HOH316 5.0 30.0 0.8 C A:THR74 5.0 14.2 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:40.5 occ:1.00 N A:ARG8 3.1 19.1 1.0 CB A:LYS7 3.7 26.7 1.0 CG A:ARG8 3.7 19.3 1.0 CA A:LYS7 3.7 19.3 1.0 CD A:LYS7 3.9 51.2 1.0 CB A:ARG8 3.9 17.3 1.0 C A:LYS7 3.9 18.4 1.0 CD A:ARG8 4.1 23.9 1.0 CA A:ARG8 4.2 16.6 1.0 O A:HOH317 4.2 23.0 0.5 CG A:LYS7 4.4 37.2 1.0 NH2 B:ARG87 4.4 17.1 1.0 NE A:ARG8 4.6 25.8 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl102 b:23.9 occ:0.75 NE1 B:TRP6 3.2 18.0 1.0 O A:HOH333 3.2 21.4 1.0 CZ2 B:TRP6 3.9 17.9 1.0 CE2 B:TRP6 3.9 17.4 1.0 CG2 B:THR4 4.3 26.4 1.0 CD1 B:TRP6 4.4 17.6 1.0 CB B:THR4 4.9 20.9 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold 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-042-17A, 3-Phenylhexahydro-2H- Cyclopenta[D]Oxazol-2-One with A Bicyclic Oxazolidinone Scaffold As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl103 b:21.4 occ:0.75 O B:HOH242 2.9 30.7 1.0 ND2 B:ASN88 3.2 14.9 1.0 N B:THR74 3.2 14.6 1.0 CA B:GLY73 3.8 15.8 1.0 OG1 B:THR74 3.8 19.1 1.0 CB B:THR74 3.9 16.3 1.0 CB B:ASN88 3.9 15.7 1.0 C B:GLY73 4.0 14.8 1.0 CG B:ASN88 4.0 13.8 1.0 CA B:THR74 4.1 15.6 1.0 O B:HOH227 4.1 19.1 1.0 NE2 B:GLN92 4.2 22.2 1.0 CD2 B:LEU89 4.4 18.4 1.0 O B:ASN88 4.5 20.6 1.0 O B:THR74 4.8 14.8 1.0 C B:ASN88 4.8 13.7 1.0 CA B:ASN88 4.8 14.0 1.0 O B:HOH203 5.0 39.9 1.0

A.K.Ghosh, J.N.Williams, R.Y.Ho, H.M.Simpson, S.I.Hattori, H.Hayashi, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Design and Synthesis of Potent Hiv-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold As the P2 Ligands: Structure-Activity Studies and Biological and X-Ray Structural Studies. J. Med. Chem. V. 61 9722 2018.
ISSN: ISSN 1520-4804
PubMed: 30354121
DOI: 10.1021/ACS.JMEDCHEM.8B01227