Cadmium in PDB 3ao5: Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase, PDB code: 3ao5 was solved by J.Wielens, S.J.Headey, M.W.Parker, D.K.Chalmers, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 1.80
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	49.032, 49.032, 103.724, 90.00, 90.00, 120.00
R / Rfree (%)	24.3 / 28.9

The structure of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Bromine	(Br)	2 atoms

The binding sites of Cadmium atom in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase (pdb code 3ao5). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase, PDB code: 3ao5:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1001 b:20.2 occ:1.00 OE1 A:GLU92 2.1 21.8 1.0 NE2 A:HIS67 2.3 17.4 1.0 SG A:CYS65 2.5 16.8 1.0 CD A:GLU92 3.0 22.8 1.0 OE2 A:GLU92 3.1 24.3 1.0 CE1 A:HIS67 3.2 20.8 1.0 CD2 A:HIS67 3.4 23.6 1.0 CB A:CYS65 3.4 20.4 1.0 O A:HOH38 3.4 17.9 1.0 CD A:CD1002 3.7 20.2 1.0 ND1 A:HIS67 4.4 20.9 1.0 CG A:GLU92 4.4 18.6 1.0 CG A:HIS67 4.5 21.1 1.0 CA A:CYS65 4.7 20.2 1.0 C A:CYS65 4.7 21.8 1.0 O A:CYS65 4.9 18.8 1.0 CB A:GLU92 4.9 19.0 1.0 O3 A:SO4752 4.9 36.4 1.0

Cadmium binding site 2 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1002 b:20.2 occ:1.00 OE2 A:GLU92 2.3 24.3 1.0 OD2 A:ASP116 2.4 21.8 1.0 O A:HOH38 2.4 17.9 1.0 O A:HOH12 2.4 17.0 1.0 CL A:CL501 2.6 19.7 1.0 SG A:CYS65 2.6 16.8 1.0 CG A:ASP116 3.3 19.4 1.0 CD A:GLU92 3.4 22.8 1.0 CB A:CYS65 3.5 20.4 1.0 OD1 A:ASP116 3.5 15.4 1.0 CD A:CD1001 3.7 20.2 1.0 OE1 A:GLU92 4.0 21.8 1.0 O A:HOH21 4.0 16.7 1.0 OD1 A:ASN120 4.2 20.4 1.0 O A:HOH4 4.3 19.9 1.0 O A:HOH13 4.5 19.3 1.0 N A:CYS65 4.5 22.7 1.0 CG A:GLU92 4.5 18.6 1.0 CA A:CYS65 4.6 20.2 1.0 CB A:ASP116 4.7 17.7 1.0 ND2 A:ASN120 4.8 19.1 1.0 CG A:ASN120 4.9 19.6 1.0 CE2 A:PHE121 4.9 19.6 1.0

Cadmium binding site 3 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1003 b:20.5 occ:1.00 OE1 B:GLU92 2.2 19.8 1.0 NE2 B:HIS67 2.3 15.8 1.0 SG B:CYS65 2.5 17.4 1.0 CD B:GLU92 2.9 22.3 1.0 OE2 B:GLU92 3.0 23.3 1.0 CE1 B:HIS67 3.3 21.3 1.0 CD2 B:HIS67 3.3 23.1 1.0 CB B:CYS65 3.4 18.6 1.0 O B:HOH23 3.5 17.9 1.0 CD B:CD1004 3.7 20.3 1.0 CG B:GLU92 4.4 18.0 1.0 ND1 B:HIS67 4.4 21.5 1.0 CG B:HIS67 4.4 22.1 1.0 CA B:CYS65 4.7 19.6 1.0 C B:CYS65 4.8 21.8 1.0 O2 B:SO4756 4.9 31.7 1.0 O B:CYS65 4.9 21.7 1.0 CG2 B:VAL72 4.9 21.4 1.0 CB B:GLU92 4.9 16.0 1.0

Cadmium binding site 4 out of 4 in the Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Fragment-Based Approach to the Design of Ligands Targeting A Novel Site on Hiv-1 Integrase within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1004 b:20.3 occ:1.00 OD2 B:ASP116 2.3 22.7 1.0 OE2 B:GLU92 2.3 23.3 1.0 O B:HOH23 2.4 17.9 1.0 O B:HOH17 2.4 17.5 1.0 CL B:CL502 2.5 20.6 1.0 SG B:CYS65 2.6 17.4 1.0 CG B:ASP116 3.2 18.7 1.0 CD B:GLU92 3.4 22.3 1.0 OD1 B:ASP116 3.5 14.3 1.0 CB B:CYS65 3.6 18.6 1.0 CD B:CD1003 3.7 20.5 1.0 OE1 B:GLU92 4.0 19.8 1.0 OD1 B:ASN120 4.2 19.0 1.0 O B:HOH49 4.4 26.8 1.0 N B:CYS65 4.5 19.8 1.0 CG B:GLU92 4.5 18.0 1.0 O B:HOH5 4.5 18.3 1.0 OD1 B:ASP64 4.5 23.6 1.0 CB B:ASP116 4.6 18.7 1.0 CA B:CYS65 4.7 19.6 1.0 ND2 B:ASN120 4.8 16.5 1.0 CG B:ASN120 4.9 18.6 1.0

J.Wielens, S.J.Headey, J.J.Deadman, D.I.Rhodes, M.W.Parker, D.K.Chalmers, M.J.Scanlon. Fragment-Based Design of Ligands Targeting A Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus 1 Chemmedchem V. 6 258 2011.
ISSN: ISSN 1860-7179
PubMed: 21275048
DOI: 10.1002/CMDC.201000483