Bromine in PDB 3nfa: 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: 3nfa 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)	18.91 / 1.95
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	71.474, 71.474, 66.833, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 20.4

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

Bromine binding site 1 out of 4 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 Bromine with other atoms in the Br 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:Br213 b:36.9 occ:0.50 BR8 A:CBJ213 0.0 36.9 0.5 C7 A:CBJ213 1.9 35.0 0.5 C6 A:CBJ213 2.8 33.7 0.5 C9 A:CBJ213 2.9 33.4 0.5 CG A:LEU158 3.1 42.5 0.7 ND1 A:HIS183 3.4 36.0 1.0 CD2 A:LEU158 3.4 40.0 0.7 CG A:HIS183 3.7 34.9 1.0 CA A:LEU158 3.7 24.9 0.3 N A:LEU158 3.8 28.8 0.3 N A:LEU158 3.8 37.2 0.7 CA A:LEU158 3.8 34.3 0.7 CB A:HIS183 3.8 26.1 1.0 CB A:LEU158 3.8 19.7 0.3 CB A:LEU158 3.9 38.0 0.7 CD1 A:LEU158 4.0 41.0 0.7 C5 A:CBJ213 4.1 34.3 0.5 O A:MET154 4.2 34.6 1.0 CD1 A:ILE161 4.2 39.3 1.0 CE1 A:HIS183 4.2 39.1 1.0 CD1 A:LEU158 4.2 14.4 0.3 C10 A:CBJ213 4.2 33.7 0.5 C A:GLU157 4.3 34.1 1.0 CD1 A:ILE84 4.4 28.3 1.0 CB A:GLU157 4.4 36.8 1.0 CG A:MET154 4.5 54.2 1.0 CD2 A:HIS183 4.5 27.6 1.0 CG A:GLU157 4.5 38.3 0.7 CG A:LEU158 4.6 14.9 0.3 C11 A:CBJ213 4.7 36.5 0.5 O A:GLU157 4.7 33.3 1.0 NE2 A:HIS183 4.8 29.8 1.0 CA A:GLU157 5.0 33.4 1.0

Bromine binding site 2 out of 4 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 Bromine with other atoms in the Br 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:Br235 b:30.3 occ:0.80 BR8 A:CBJ235 0.0 30.3 0.8 C7 A:CBJ235 1.9 27.9 0.8 C6 A:CBJ235 2.5 34.6 0.8 C9 A:CBJ235 3.1 28.7 0.8 CB B:TRP132 3.6 21.5 1.0 CG B:TRP132 3.7 23.0 1.0 CE A:MET178 3.8 25.4 1.0 C5 A:CBJ235 3.8 38.7 0.8 CA B:ALA129 3.8 22.0 1.0 CD2 B:LEU102 3.8 20.8 1.0 CD2 B:TRP132 4.0 19.2 1.0 CD1 B:LEU102 4.0 21.8 1.0 CB B:ALA129 4.0 22.8 1.0 CE3 B:TRP132 4.1 23.7 1.0 C10 A:CBJ235 4.3 33.8 0.8 CG B:LEU102 4.3 23.7 1.0 CB B:LEU102 4.4 18.6 1.0 O B:ALA129 4.4 20.3 1.0 CD1 B:TRP132 4.5 21.5 1.0 O A:HOH247 4.5 52.5 1.0 C11 A:CBJ235 4.5 39.3 0.8 C B:ALA129 4.6 24.2 1.0 CG A:MET178 4.6 24.2 1.0 N B:ALA129 4.8 22.0 1.0 O B:ALA128 4.8 22.7 1.0 CE2 B:TRP132 4.9 18.2 1.0 C3 A:CBJ235 4.9 44.8 0.8 CA B:TRP132 5.0 24.3 1.0

Bromine binding site 3 out of 4 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 Bromine with other atoms in the Br 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 B:Br222 b:48.3 occ:0.70 BR8 B:CBJ222 0.0 48.3 0.7 C7 B:CBJ222 1.9 48.4 0.7 C6 B:CBJ222 2.8 45.7 0.7 C9 B:CBJ222 2.9 46.9 0.7 CG B:LEU158 3.1 40.9 0.7 CD2 B:LEU158 3.2 33.1 0.7 ND1 B:HIS183 3.5 38.2 1.0 CA B:LEU158 3.6 24.4 0.3 N B:LEU158 3.6 28.1 0.3 N B:LEU158 3.6 34.3 0.7 CA B:LEU158 3.6 31.0 0.7 CG B:HIS183 3.7 34.0 1.0 CB B:LEU158 3.8 20.6 0.3 CB B:HIS183 3.8 25.8 1.0 CB B:LEU158 3.8 36.4 0.7 C5 B:CBJ222 4.0 46.8 0.7 CD1 B:ILE161 4.1 39.0 1.0 O B:MET154 4.1 33.8 1.0 C B:GLU157 4.2 33.1 1.0 CD1 B:LEU158 4.2 14.6 0.3 C10 B:CBJ222 4.2 51.4 0.7 CE1 B:HIS183 4.2 41.6 1.0 CG B:GLU157 4.2 44.2 1.0 CD1 B:LEU158 4.3 39.5 0.7 CB B:GLU157 4.3 39.5 1.0 CD1 B:ILE84 4.4 26.5 1.0 CG B:MET154 4.5 53.0 1.0 CD2 B:HIS183 4.6 28.2 1.0 O B:GLU157 4.6 32.3 1.0 CG B:LEU158 4.6 15.8 0.3 C11 B:CBJ222 4.7 51.6 0.7 NE2 B:HIS183 4.8 31.0 1.0 CA B:GLU157 4.9 32.1 1.0

Bromine binding site 4 out of 4 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 Bromine with other atoms in the Br 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 B:Br245 b:30.6 occ:0.80 BR8 B:CBJ245 0.0 30.6 0.8 C7 B:CBJ245 1.9 29.8 0.8 C6 B:CBJ245 2.5 35.2 0.8 C9 B:CBJ245 3.1 32.6 0.8 CB A:TRP132 3.6 23.0 1.0 CG A:TRP132 3.7 22.7 1.0 C5 B:CBJ245 3.8 38.1 0.8 CE B:MET178 3.8 27.6 1.0 CA A:ALA129 3.9 21.8 1.0 CD2 A:LEU102 3.9 22.0 1.0 CD2 A:TRP132 4.0 18.4 1.0 CD1 A:LEU102 4.0 21.1 1.0 CB A:ALA129 4.1 22.6 1.0 CE3 A:TRP132 4.2 25.1 1.0 C10 B:CBJ245 4.3 37.9 0.8 CG A:LEU102 4.3 23.1 1.0 CB A:LEU102 4.3 17.6 1.0 O A:ALA129 4.4 20.3 1.0 CD1 A:TRP132 4.5 21.0 1.0 O A:HOH246 4.5 48.4 1.0 C11 B:CBJ245 4.6 42.3 0.8 CG B:MET178 4.6 23.6 1.0 C A:ALA129 4.6 24.1 1.0 N A:ALA129 4.8 20.6 1.0 CE2 A:TRP132 4.9 19.6 1.0 O A:ALA128 4.9 22.3 1.0 C3 B:CBJ245 5.0 44.6 0.8 CA A:TRP132 5.0 23.7 1.0

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