Chlorine in PDB 5upz: Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz 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 / 1.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.175, 86.418, 45.828, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 19.8

The structure of Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group 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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group (pdb code 5upz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group, PDB code: 5upz:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:12.4 occ:0.80 O A:HOH417 2.9 31.1 0.5 O A:HOH324 3.0 24.9 1.0 N A:THR74 3.2 10.6 1.0 ND2 A:ASN88 3.2 9.9 1.0 CA A:GLY73 3.7 10.7 1.0 CB A:ASN88 3.8 8.4 1.0 OG1 A:THR74 3.8 13.5 1.0 CB A:THR74 3.9 12.4 1.0 C A:GLY73 4.0 10.1 1.0 CG A:ASN88 4.0 9.1 1.0 CA A:THR74 4.2 11.2 1.0 O A:HOH344 4.3 21.5 1.0 O A:HOH363 4.3 25.8 0.5 O A:ASN88 4.7 10.0 1.0 OD1 A:ASP30 4.8 24.9 1.0 O A:THR74 4.8 11.0 1.0 CA A:ASN88 4.9 8.4 1.0

Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl102 b:14.3 occ:0.80 O B:HOH326 3.2 24.8 1.0 O A:HOH356 3.2 12.6 1.0 NE1 B:TRP6 3.3 11.2 1.0 CZ2 B:TRP6 3.9 10.9 1.0 CE2 B:TRP6 3.9 10.5 1.0 CG2 B:THR4 4.3 16.4 1.0 CD1 B:TRP6 4.5 10.6 1.0 CB B:THR4 4.9 11.4 1.0 O B:HOH250 4.9 19.3 0.5

Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group


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-0518A , An Isophthalamide-Derived P2-P3 Ligand with the Para-Hydoxymethyl Sulfonamide Isostere As the P2' Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl103 b:15.4 occ:0.80 O B:HOH231 2.9 17.3 1.0 ND2 B:ASN88 3.1 10.5 1.0 N B:THR74 3.1 9.0 1.0 O B:HOH321 3.2 28.4 1.0 OG1 B:THR74 3.7 13.0 1.0 CA B:GLY73 3.8 10.3 1.0 CB B:THR74 3.8 10.1 1.0 CB B:ASN88 3.8 9.9 1.0 C B:GLY73 4.0 9.2 1.0 CG B:ASN88 4.0 9.0 1.0 O B:HOH245 4.1 13.8 1.0 CA B:THR74 4.1 9.3 1.0 NE2 B:GLN92 4.4 10.9 1.0 O B:ASN88 4.5 11.4 1.0 CD2 B:LEU89 4.6 13.5 1.0 O B:THR74 4.7 9.9 1.0 C B:ASN88 4.8 9.9 1.0 CA B:ASN88 4.8 8.9 1.0 O B:HOH220 4.9 28.5 1.0 C B:THR74 5.0 9.0 1.0

A.K.Ghosh, M.Brindisi, P.R.Nyalapatla, J.Takayama, J.R.Ella-Menye, S.Yashchuk, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Design of Novel Hiv-1 Protease Inhibitors Incorporating Isophthalamide-Derived P2-P3 Ligands: Synthesis, Biological Evaluation and X-Ray Structural Studies of Inhibitor-Hiv-1 Protease Complex. Bioorg. Med. Chem. V. 25 5114 2017.
ISSN: ESSN 1464-3391
PubMed: 28434781
DOI: 10.1016/J.BMC.2017.04.005