Chlorine in PDB 6vod: Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand, PDB code: 6vod 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)	33.43 / 1.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.784, 86.209, 46.015, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 18.5

The structure of Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand (pdb code 6vod). 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand, PDB code: 6vod:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:16.6 occ:1.00 O A:HOH692 3.0 31.2 1.0 N A:THR74 3.2 10.1 1.0 ND2 A:ASN88 3.2 10.5 1.0 CA A:GLY73 3.7 10.6 1.0 CB A:ASN88 3.8 8.6 1.0 OG1 A:THR74 3.8 13.7 1.0 CB A:THR74 3.8 12.1 1.0 C A:GLY73 4.0 10.2 1.0 CG A:ASN88 4.0 9.5 1.0 CA A:THR74 4.1 9.7 1.0 O A:HOH644 4.3 17.9 1.0 O A:ASN88 4.6 10.0 1.0 O A:THR74 4.8 10.3 1.0 CA A:ASN88 4.9 8.3 1.0 C A:THR74 5.0 9.5 1.0

Chlorine binding site 2 out of 2 in the Hiv-1 Wild Type Protease with Grl-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative 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-052-16A, A Tricyclic Cyclohexane Fused Tetrahydrofuranofuran (Chf-Thf) Derivative As the P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:16.8 occ:1.00 O A:HOH641 3.3 13.2 1.0 NE1 B:TRP6 3.3 11.5 1.0 CZ2 B:TRP6 3.9 11.1 1.0 CE2 B:TRP6 3.9 10.6 1.0 CG2 B:THR4 4.3 16.8 1.0 CD1 B:TRP6 4.5 11.7 1.0 O B:HOH348 4.8 31.8 1.0 CB B:THR4 4.9 12.3 1.0

A.K.Ghosh, S.Kovela, H.L.Osswald, M.Amano, M.Aoki, J.Agniswamy, Y.F.Wang, I.T.Weber, H.Mitsuya. Structure-Based Design of Highly Potent Hiv-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-Ray Structural Studies. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32348139
DOI: 10.1021/ACS.JMEDCHEM.0C00202