Chlorine in PDB 3vf7: Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031

All present enzymatic activity of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031:
3.4.23.16;

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7 was solved by X.X.Yu, Y.F.Wang, Y.C.E.Chang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.820, 86.242, 46.005, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.5

The structure of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 (pdb code 3vf7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031, PDB code: 3vf7:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:11.9 occ:0.75 C1 A:GOL206 2.6 23.4 0.2 NE1 A:TRP6 3.2 11.5 1.0 O B:HOH604 3.3 12.4 1.0 O1 A:GOL206 3.3 20.7 0.2 CZ2 A:TRP6 3.8 10.5 1.0 CE2 A:TRP6 3.9 9.7 1.0 C2 A:GOL206 3.9 25.8 0.2 CG2 A:THR4 4.2 16.7 1.0 CD1 A:TRP6 4.4 10.8 1.0 O A:HOH1042 4.6 28.6 1.0 O2 A:GOL206 4.8 28.4 0.2 CB A:THR4 4.8 12.2 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:16.8 occ:1.00 O A:HOH1015 3.0 16.0 1.0 ND2 A:ASN88 3.2 10.8 1.0 N A:THR74 3.2 9.4 1.0 OG1 A:THR74 3.7 12.8 1.0 CA A:GLY73 3.8 10.0 1.0 CB A:THR74 3.8 10.7 1.0 C2 A:GOL205 3.8 29.3 0.5 CB A:ASN88 3.9 10.2 1.0 C1 A:GOL205 3.9 29.1 0.5 C A:GLY73 4.0 8.7 1.0 CG A:ASN88 4.0 9.1 1.0 CA A:THR74 4.1 9.6 1.0 O A:HOH1009 4.1 13.2 1.0 O2 A:GOL205 4.2 38.6 0.5 NE2 A:GLN92 4.4 12.2 1.0 O A:ASN88 4.6 12.4 1.0 CD2 A:LEU89 4.6 14.9 1.0 O A:THR74 4.7 9.9 1.0 C A:ASN88 4.8 10.1 1.0 CA A:ASN88 4.8 8.8 1.0 C A:THR74 4.9 9.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Hiv-1 Protease Mutant L76V with Novel P1'-Ligands Grl-02031 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl502 b:13.6 occ:1.00 N B:THR74 3.2 9.7 1.0 ND2 B:ASN88 3.3 12.0 1.0 CA B:GLY73 3.8 10.2 1.0 CB B:ASN88 3.8 8.9 1.0 OG1 B:THR74 3.9 14.6 1.0 CB B:THR74 3.9 12.3 1.0 C B:GLY73 4.0 10.2 1.0 CG B:ASN88 4.1 9.5 1.0 CA B:THR74 4.2 9.5 1.0 O B:HOH614 4.4 21.8 1.0 O B:THR74 4.7 10.8 1.0 O B:ASN88 4.7 10.4 1.0 CA B:ASN88 4.9 8.7 1.0 C B:THR74 5.0 9.4 1.0

Y.C.Chang, X.Yu, Y.Zhang, Y.Tie, Y.F.Wang, S.Yashchuk, A.K.Ghosh, R.W.Harrison, I.T.Weber. Potent Antiviral Hiv-1 Protease Inhibitor Grl-02031 Adapts to the Structures of Drug Resistant Mutants with Its P1'-Pyrrolidinone Ring. J.Med.Chem. V. 55 3387 2012.
ISSN: ISSN 0022-2623
PubMed: 22401672
DOI: 10.1021/JM300072D