Chlorine in PDB 6e9a: Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a 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 / 1.22
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.372, 86.276, 46.020, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18.8

The structure of Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand (pdb code 6e9a). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand, PDB code: 6e9a:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:15.2 occ:1.00 O A:HOH690 2.9 29.8 0.2 N A:THR74 3.2 11.3 1.0 ND2 A:ASN88 3.2 11.3 1.0 CA A:GLY73 3.8 11.9 1.0 CB A:ASN88 3.8 11.0 1.0 OG1 A:THR74 3.8 14.5 1.0 CB A:THR74 3.9 11.6 1.0 C A:GLY73 4.0 10.5 1.0 CG A:ASN88 4.1 11.1 1.0 O A:HOH626 4.1 33.4 0.5 CA A:THR74 4.2 10.5 1.0 O A:HOH632 4.4 18.6 1.0 O A:ASN88 4.7 11.9 1.0 O A:THR74 4.7 11.5 1.0 CA A:ASN88 4.9 10.3 1.0 C A:THR74 5.0 10.5 1.0

Chlorine binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff 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-034-17A, (3AS, 5R, 6AR)-2-Oxohexahyd Cyclopenta[D]-5-Oxazolyl Urethane with A Bicyclic Oxazolidinone Scaff As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:19.8 occ:1.00 O B:HOH390 3.2 26.1 0.5 NE1 B:TRP6 3.3 13.2 1.0 O A:HOH633 3.3 14.9 1.0 CZ2 B:TRP6 3.8 13.7 1.0 CE2 B:TRP6 3.9 13.3 1.0 CG2 B:THR4 4.3 19.5 1.0 CD1 B:TRP6 4.4 13.0 1.0 O B:HOH366 4.6 22.9 0.5 CB B:THR4 4.8 14.7 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