Chlorine in PDB 4zip: Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand)

All present enzymatic activity of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand):
3.4.23.16;

The structure of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand), PDB code: 4zip 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 / 1.11
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.000, 86.280, 46.130, 90.00, 90.00, 90.00
R / Rfree (%)	13 / 15.5

The structure of Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Chlorine atom in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived P2- Ligand) (pdb code 4zip). 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-0648A (A Isophthalamide-Derived P2- Ligand), PDB code: 4zip:
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-0648A (A Isophthalamide-Derived 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-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:11.6 occ:1.00 N A:THR74 3.2 8.7 1.0 ND2 A:ASN88 3.3 8.7 1.0 CA A:GLY73 3.8 8.4 1.0 CB A:ASN88 3.8 7.7 1.0 OG1 A:THR74 3.8 12.3 1.0 CB A:THR74 3.9 9.7 1.0 C A:GLY73 4.0 8.2 1.0 CG A:ASN88 4.0 7.8 1.0 CA A:THR74 4.1 8.8 1.0 O A:HOH639 4.3 29.0 0.5 O A:HOH643 4.3 15.3 1.0 O A:ASN88 4.7 8.7 1.0 O A:THR74 4.8 9.4 1.0 CA A:ASN88 4.9 7.2 1.0 C A:THR74 5.0 8.6 1.0

Chlorine binding site 2 out of 3 in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived 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-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl204 b:13.5 occ:1.00 O B:HOH424 3.2 24.7 1.0 O A:HOH644 3.3 10.8 1.0 NE1 B:TRP6 3.3 9.4 1.0 CZ2 B:TRP6 3.8 9.0 1.0 CE2 B:TRP6 3.9 8.7 1.0 CG2 B:THR4 4.2 15.0 1.0 CD1 B:TRP6 4.5 9.3 1.0 O B:HOH350 4.8 19.0 0.5 CB B:THR4 4.9 11.2 1.0

Chlorine binding site 3 out of 3 in the Hiv-1 Wild Type Protease with Grl-0648A (A Isophthalamide-Derived 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-0648A (A Isophthalamide-Derived P2- Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl205 b:16.4 occ:1.00 O B:HOH329 2.9 13.6 1.0 O B:HOH417 3.1 37.0 1.0 N B:THR74 3.1 7.3 1.0 ND2 B:ASN88 3.2 8.5 1.0 OG1 B:THR74 3.7 11.4 1.0 CA B:GLY73 3.8 8.4 1.0 CB B:THR74 3.8 8.8 1.0 CB B:ASN88 3.9 7.9 1.0 C B:GLY73 3.9 7.4 1.0 CG B:ASN88 4.0 7.7 1.0 CA B:THR74 4.1 8.0 1.0 O B:HOH352 4.1 12.3 1.0 NE2 B:GLN92 4.4 9.4 1.0 O B:HOH368 4.4 38.1 1.0 O B:ASN88 4.4 9.3 1.0 CD2 B:LEU89 4.6 11.8 1.0 O B:THR74 4.7 8.1 1.0 C B:ASN88 4.8 7.4 1.0 O B:HOH333 4.8 26.1 0.8 CA B:ASN88 4.8 7.1 1.0 C B:THR74 4.9 7.3 1.0

A.K.Ghosh, J.Takayama, L.A.Kassekert, J.R.Ella-Menye, S.Yashchuk, J.Agniswamy, Y.F.Wang, M.Aoki, M.Amano, I.T.Weber, H.Mitsuya. Structure-Based Design, Synthesis, X-Ray Studies, and Biological Evaluation of Novel Hiv-1 Protease Inhibitors Containing Isophthalamide-Derived P2-Ligands. Bioorg.Med.Chem.Lett. V. 25 4903 2015.
ISSN: ESSN 1464-3405
PubMed: 26096678
DOI: 10.1016/J.BMCL.2015.05.052