Chlorine in PDB 6c8y: D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir

The structure of D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir, PDB code: 6c8y was solved by I.W.Windsor, R.T.Raines, K.T.Forest, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.79 / 1.94
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	59.118, 86.410, 45.793, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22

The binding sites of Chlorine atom in the D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir (pdb code 6c8y). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir, PDB code: 6c8y:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:22.8 occ:1.00 O A:HOH262 3.0 35.5 1.0 ND2 A:ASN88 3.2 17.7 1.0 N A:THR74 3.3 20.0 1.0 CA A:GLY73 3.8 16.1 1.0 CB A:ASN88 3.9 17.2 1.0 OG1 A:THR74 3.9 19.8 1.0 CB A:THR74 4.0 18.4 1.0 CG A:ASN88 4.0 24.7 1.0 C A:GLY73 4.1 18.3 1.0 O A:HOH236 4.2 27.2 1.0 CA A:THR74 4.2 16.5 1.0 O A:ASN88 4.6 15.2 1.0 CA A:ASN88 4.9 15.0 1.0 O A:THR74 4.9 15.1 1.0 C A:ASN88 5.0 17.4 1.0

Chlorine binding site 2 out of 3 in the D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl201 b:25.2 occ:1.00 NE1 B:TRP106 3.3 16.5 1.0 O A:HOH226 3.3 19.8 1.0 CZ2 B:TRP106 3.9 19.6 1.0 CE2 B:TRP106 3.9 16.5 1.0 CG2 B:THR104 4.3 20.5 1.0 CD1 B:TRP106 4.5 14.6 1.0 CB B:THR104 4.9 20.6 1.0

Chlorine binding site 3 out of 3 in the D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of D30N Hiv-1 Protease in Complex with A Phenylboronic Acid (P2') Analog of Darunavir within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:28.4 occ:1.00 O B:HOH342 2.9 26.1 1.0 ND2 B:ASN188 3.1 12.2 1.0 N B:THR174 3.1 16.6 1.0 CA B:GLY173 3.7 15.3 1.0 OG1 B:THR174 3.8 21.1 1.0 CB B:THR174 3.8 21.2 1.0 CB B:ASN188 3.9 13.6 1.0 C B:GLY173 3.9 23.6 1.0 CG B:ASN188 4.0 15.8 1.0 CA B:THR174 4.1 17.1 1.0 O B:HOH338 4.2 20.6 1.0 NE2 B:GLN192 4.3 20.4 1.0 O B:ASN188 4.4 17.9 1.0 CD2 B:LEU189 4.4 16.3 1.0 O B:THR174 4.7 13.7 1.0 C B:ASN188 4.7 19.5 1.0 O B:HOH360 4.8 19.2 1.0 CA B:ASN188 4.8 14.1 1.0 C B:THR174 4.9 15.6 1.0

I.W.Windsor, M.J.Palte, J.C.Lukesh 3Rd., B.Gold, K.T.Forest, R.T.Raines. Sub-Picomolar Inhibition of Hiv-1 Protease with A Boronic Acid. J. Am. Chem. Soc. V. 140 14015 2018.
ISSN: ESSN 1520-5126
PubMed: 30346745
DOI: 10.1021/JACS.8B07366