Chlorine in PDB 3nf8: Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design

The structure of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design, PDB code: 3nf8 was solved by T.S.Peat, J.Newman, J.J.Deadman, D.Rhodes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.52 / 1.90
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	71.549, 71.549, 67.099, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.8

The binding sites of Chlorine atom in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design (pdb code 3nf8). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design, PDB code: 3nf8:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl225 b:55.2 occ:0.70 CL25 A:CDQ225 0.0 55.2 0.7 C1 A:CDQ225 1.7 48.4 0.7 C6 A:CDQ225 2.7 46.6 0.7 C2 A:CDQ225 2.7 43.2 0.7 OD2 A:ASP207 3.6 68.2 1.0 N A:GLY59 3.8 30.1 1.0 C5 A:CDQ225 3.9 46.3 0.7 O A:HOH220 3.9 42.4 1.0 CA A:GLY59 4.0 27.5 1.0 C3 A:CDQ225 4.0 43.5 0.7 CG A:PRO58 4.1 41.1 1.0 C A:PRO58 4.5 33.4 1.0 C4 A:CDQ225 4.5 43.9 0.7 CB A:PRO58 4.6 38.8 1.0 CG A:ASP207 4.7 64.0 1.0 O A:PRO109 4.7 34.2 1.0 CB A:PRO109 4.8 26.7 1.0 CB A:LYS111 4.8 27.8 1.0 O A:PRO58 5.0 32.3 1.0

Chlorine binding site 2 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl247 b:45.8 occ:0.70 CL25 A:CDQ247 0.0 45.8 0.7 C1 A:CDQ247 1.7 36.5 0.7 C2 A:CDQ247 2.6 36.6 0.7 C6 A:CDQ247 2.8 37.4 0.7 CG1 A:VAL77 3.9 14.4 0.5 C3 A:CDQ247 3.9 34.7 0.7 OE1 A:GLN62 3.9 38.8 0.5 C5 A:CDQ247 4.0 34.1 0.7 CB A:GLN62 4.1 20.3 0.5 CD A:GLN62 4.2 30.6 0.5 CG2 A:VAL79 4.2 28.2 1.0 CB A:GLN62 4.2 21.9 0.5 CG1 A:VAL150 4.4 45.4 1.0 CG A:GLN62 4.4 19.7 0.5 C4 A:CDQ247 4.4 35.9 0.7 CG1 A:VAL79 4.4 31.3 1.0 CG A:GLN62 4.5 26.7 0.5 CG1 A:VAL77 4.6 20.2 0.5 CB A:VAL79 4.7 23.8 1.0 CB A:VAL77 4.7 19.9 0.5 CA A:VAL79 4.8 23.9 1.0 CG1 A:ILE151 4.8 45.8 1.0 NE2 A:GLN62 4.8 35.9 0.5

Chlorine binding site 3 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl267 b:37.4 occ:0.70 CL25 A:CDQ267 0.0 37.4 0.7 C1 A:CDQ267 1.7 32.2 0.7 C2 A:CDQ267 2.7 32.6 0.7 C6 A:CDQ267 2.7 27.9 0.7 CB B:TRP132 3.2 19.2 1.0 CG B:TRP132 3.4 22.2 1.0 CE A:MET178 3.5 31.6 1.0 CD2 B:TRP132 3.7 19.3 1.0 CA B:ALA129 3.9 18.6 1.0 C3 A:CDQ267 4.0 33.1 0.7 C5 A:CDQ267 4.0 31.6 0.7 CE3 B:TRP132 4.0 21.6 1.0 CD1 B:TRP132 4.0 24.0 1.0 CD1 B:LEU102 4.1 23.9 1.0 CB B:ALA129 4.3 19.2 1.0 CD2 B:LEU102 4.3 24.6 1.0 C4 A:CDQ267 4.4 30.7 0.7 O B:ALA129 4.4 19.6 1.0 O B:ALA128 4.5 20.7 1.0 CE2 B:TRP132 4.6 19.4 1.0 CG A:MET178 4.6 21.8 1.0 C B:ALA129 4.7 19.4 1.0 N B:ALA129 4.7 19.0 1.0 CG B:LEU102 4.7 22.4 1.0 CA B:TRP132 4.7 21.9 1.0 NE1 B:TRP132 4.7 18.9 1.0 SD A:MET178 4.8 31.8 1.0 CB B:LEU102 4.9 18.6 1.0 C B:ALA128 5.0 21.5 1.0

Chlorine binding site 4 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl277 b:56.2 occ:0.70 CL25 A:CDQ277 0.0 56.2 0.7 C1 A:CDQ277 1.7 49.0 0.7 C6 A:CDQ277 2.7 45.7 0.7 C2 A:CDQ277 2.7 42.9 0.7 OD2 B:ASP207 3.7 68.9 1.0 C5 A:CDQ277 3.9 46.3 0.7 N B:GLY59 3.9 29.8 1.0 CG B:PRO58 4.0 39.3 1.0 O B:HOH231 4.0 44.6 1.0 C3 A:CDQ277 4.0 44.0 0.7 CA B:GLY59 4.0 27.9 1.0 C4 A:CDQ277 4.5 44.7 0.7 C B:PRO58 4.5 33.9 1.0 CB B:PRO58 4.6 38.2 1.0 O B:PRO109 4.7 34.5 1.0 CB B:LYS111 4.7 23.1 0.5 CB B:PRO109 4.8 28.0 1.0 CD B:PRO58 4.9 40.9 1.0 CG B:ASP207 4.9 66.4 1.0 CD B:LYS111 4.9 35.4 0.5

Chlorine binding site 5 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl235 b:34.2 occ:0.70 CL25 B:CDQ235 0.0 34.2 0.7 C1 B:CDQ235 1.7 31.1 0.7 C2 B:CDQ235 2.7 31.8 0.7 C6 B:CDQ235 2.7 29.1 0.7 CB A:TRP132 3.2 19.2 1.0 CG A:TRP132 3.4 22.0 1.0 CE B:MET178 3.6 33.2 1.0 CD2 A:TRP132 3.7 18.7 1.0 CA A:ALA129 3.9 19.3 1.0 C3 B:CDQ235 3.9 31.9 0.7 CE3 A:TRP132 4.0 20.0 1.0 C5 B:CDQ235 4.0 32.5 0.7 CD1 A:TRP132 4.1 23.7 1.0 CD1 A:LEU102 4.1 23.7 1.0 CD2 A:LEU102 4.2 24.1 1.0 CB A:ALA129 4.3 19.6 1.0 O B:HOH246 4.3 58.0 1.0 O A:ALA129 4.4 19.2 1.0 C4 B:CDQ235 4.4 30.8 0.7 CE2 A:TRP132 4.5 19.7 1.0 CG B:MET178 4.6 23.7 1.0 O A:ALA128 4.6 21.0 1.0 CG A:LEU102 4.6 23.1 1.0 C A:ALA129 4.6 19.9 1.0 N A:ALA129 4.7 19.8 1.0 CA A:TRP132 4.7 20.6 1.0 NE1 A:TRP132 4.7 21.1 1.0 SD B:MET178 4.8 32.2 1.0 CB A:LEU102 4.8 17.1 1.0 CZ3 A:TRP132 5.0 21.9 1.0

Chlorine binding site 6 out of 6 in the Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structural Basis For A New Mechanism of Inhibition of Hiv Integrase Identified By Fragment Screening and Structure Based Design within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl257 b:45.7 occ:0.70 CL25 B:CDQ257 0.0 45.7 0.7 C1 B:CDQ257 1.7 39.5 0.7 C2 B:CDQ257 2.6 39.4 0.7 C6 B:CDQ257 2.7 38.5 0.7 OE1 B:GLN62 3.7 36.7 0.4 CG1 B:VAL77 3.8 13.0 0.4 C3 B:CDQ257 3.9 39.4 0.7 C5 B:CDQ257 4.0 35.4 0.7 CB B:GLN62 4.2 20.9 0.6 CG2 B:VAL79 4.2 27.2 1.0 CG1 B:VAL150 4.2 45.2 1.0 CD B:GLN62 4.2 28.7 0.4 CG1 B:VAL79 4.3 31.6 1.0 CB B:GLN62 4.4 22.6 0.4 CG B:GLN62 4.4 22.6 0.6 C4 B:CDQ257 4.4 38.0 0.7 CG1 B:VAL77 4.5 20.8 0.6 CB B:VAL77 4.7 20.5 0.6 CB B:VAL79 4.7 24.5 1.0 CG B:GLN62 4.7 25.9 0.4 CA B:VAL79 4.7 23.8 1.0 CG1 B:ILE151 4.8 45.7 1.0 CG2 B:VAL77 5.0 14.2 0.4 NE2 B:GLN62 5.0 33.6 0.4

D.I.Rhodes, T.S.Peat, N.Vandegraaff, D.Jeevarajah, G.Le, E.D.Jones, J.A.Smith, J.A.Coates, L.J.Winfield, N.Thienthong, J.Newman, D.Lucent, J.H.Ryan, G.P.Savage, C.L.Francis, J.J.Deadman. Structural Basis For A New Mechanism of Inhibition of Hiv-1 Integrase Identified By Fragment Screening and Structure-Based Design Antivir.Chem.Chemother. V. 21 155 2011.
ISSN: ISSN 0956-3202
PubMed: 21602613
DOI: 10.3851/IMP1716