Chlorine in PDB 2qnp: Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor

All present enzymatic activity of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor:
3.4.23.16;

The structure of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnp was solved by J.Boettcher, A.Blum, A.Heine, W.E.Diederich, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.41
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.356, 85.899, 46.648, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.4

The structure of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Chlorine atom in the Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor (pdb code 2qnp). 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 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnp:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl2602 b:18.0 occ:1.00 N A:THR74 3.2 11.9 1.0 ND2 A:ASN88 3.2 12.9 1.0 CA A:GLY73 3.7 10.4 1.0 OG1 A:THR74 3.7 15.8 1.0 CB A:THR74 3.8 11.2 1.0 CB A:ASN88 3.8 10.6 1.0 C A:GLY73 3.9 15.9 1.0 CG A:ASN88 4.0 12.6 1.0 CA A:THR74 4.1 8.7 1.0 O A:HOH3067 4.2 25.1 1.0 O A:ASN88 4.6 9.2 1.0 CA A:ASN88 4.9 7.0 1.0 O A:THR74 4.9 10.3 1.0 C A:ASN88 5.0 9.0 1.0

Chlorine binding site 2 out of 3 in the Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2601 b:15.2 occ:1.00 O B:HOH3105 2.8 25.7 1.0 ND2 B:ASN88 3.2 9.0 1.0 N B:THR74 3.2 8.0 1.0 O B:HOH3180 3.5 30.1 1.0 O B:HOH3148 3.7 55.5 1.0 CA B:GLY73 3.7 9.9 1.0 CB B:ASN88 3.9 8.2 1.0 CB B:THR74 3.9 7.9 1.0 OG1 B:THR74 3.9 11.8 1.0 C B:GLY73 4.0 8.1 1.0 CG B:ASN88 4.0 7.7 1.0 CA B:THR74 4.1 7.3 1.0 O B:HOH3005 4.4 13.2 1.0 O B:HOH3177 4.5 36.1 1.0 CD2 B:LEU89 4.6 14.0 1.0 O B:THR74 4.7 9.4 1.0 O B:ASN88 4.8 12.3 1.0 C B:ASN88 4.9 10.4 1.0 CA B:ASN88 4.9 7.1 1.0 C B:THR74 5.0 8.9 1.0

Chlorine binding site 3 out of 3 in the Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease in Complex with A Iodo Decorated Pyrrolidine-Based Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl2603 b:17.5 occ:1.00 NE1 B:TRP6 3.2 12.1 1.0 O A:HOH3013 3.3 11.3 1.0 CZ2 B:TRP6 3.8 10.9 1.0 CE2 B:TRP6 3.9 8.6 1.0 CD1 B:TRP6 4.4 12.0 1.0 CG2 B:THR4 4.4 14.9 1.0 O B:HOH3096 4.6 31.4 1.0 CB B:THR4 4.9 11.4 1.0

A.Blum, J.Bottcher, A.Heine, G.Klebe, W.E.Diederich. Structure-Guided Design of C2-Symmetric Hiv-1 Protease Inhibitors Based on A Pyrrolidine Scaffold. J.Med.Chem. V. 51 2078 2008.
ISSN: ISSN 0022-2623
PubMed: 18348517
DOI: 10.1021/JM701142S