Cadmium in PDB 3ovn: 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: 3ovn was solved by J.Wielens, D.K.Chalmers, S.J.Headey, J.J.Deadman, D.K.Rhodes, M.W.Parker, M.J.Scanlon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.91 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.750, 59.704, 81.818, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 24.9

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 3ovn). 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: 3ovn:
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:Cd1003 b:24.5 occ:1.00 OE1 A:GLU92 1.9 13.8 1.0 O A:HOH217 2.1 13.8 1.0 NE2 A:HIS67 2.4 22.5 1.0 SG A:CYS65 2.5 25.0 1.0 CD A:GLU92 2.9 29.9 1.0 CD2 A:HIS67 3.1 22.1 1.0 OE2 A:GLU92 3.3 34.8 1.0 CD A:CD1004 3.5 27.2 1.0 CE1 A:HIS67 3.5 21.8 1.0 CB A:CYS65 3.5 25.6 1.0 CG A:GLU92 4.3 26.8 1.0 CG A:HIS67 4.3 25.7 1.0 ND1 A:HIS67 4.5 24.4 1.0 CA A:CYS65 4.8 25.6 1.0 C A:CYS65 4.9 25.1 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:Cd1004 b:27.2 occ:1.00 OE2 A:GLU92 2.2 34.8 1.0 OD2 A:ASP116 2.4 29.2 1.0 SG A:CYS65 2.6 25.0 1.0 O A:HOH214 2.6 15.1 1.0 CD A:GLU92 3.2 29.9 1.0 CG A:ASP116 3.3 23.0 1.0 CB A:CYS65 3.4 25.6 1.0 OD1 A:ASP116 3.5 23.9 1.0 CD A:CD1003 3.5 24.5 1.0 OE1 A:GLU92 3.6 13.8 1.0 N A:CYS65 4.5 27.5 1.0 CG A:GLU92 4.5 26.8 1.0 CA A:CYS65 4.6 25.6 1.0 O A:HOH217 4.6 13.8 1.0 CE2 A:PHE121 4.7 29.6 1.0 O A:HOH31 4.7 35.9 1.0 OD1 A:ASN120 4.7 25.4 1.0 CB A:ASP116 4.7 21.1 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:Cd1001 b:35.5 occ:1.00 OE2 B:GLU92 2.0 27.1 1.0 OD2 B:ASP116 2.3 30.1 1.0 O B:HOH217 2.4 31.4 1.0 O B:HOH40 2.5 26.2 1.0 O B:HOH214 2.6 17.0 1.0 SG B:CYS65 2.6 32.1 1.0 CD B:GLU92 3.2 25.9 1.0 CG B:ASP116 3.2 32.9 1.0 CB B:CYS65 3.3 32.0 1.0 OD1 B:ASP116 3.5 33.7 1.0 CD B:CD1002 3.5 33.9 0.9 OE1 B:GLU92 3.8 20.0 1.0 OD1 B:ASN120 4.2 32.5 1.0 CG B:GLU92 4.2 27.5 1.0 N B:CYS65 4.3 32.3 1.0 OD1 B:ASP64 4.4 44.1 1.0 O B:HOH43 4.4 29.9 1.0 O B:HOH37 4.4 34.0 1.0 CA B:CYS65 4.5 31.7 1.0 ND2 B:ASN120 4.6 30.3 1.0 CB B:ASP116 4.6 32.1 1.0 CE2 B:PHE121 4.7 26.4 1.0 CG B:ASN120 4.8 33.4 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:Cd1002 b:33.9 occ:0.90 OE1 B:GLU92 1.8 20.0 1.0 O B:HOH217 1.9 31.4 1.0 O B:HOH43 1.9 29.9 1.0 NE2 B:HIS67 2.2 37.8 1.0 SG B:CYS65 2.5 32.1 1.0 CD B:GLU92 2.7 25.9 1.0 OE2 B:GLU92 2.7 27.1 1.0 CD2 B:HIS67 3.2 39.2 1.0 CE1 B:HIS67 3.2 40.8 1.0 CB B:CYS65 3.5 32.0 1.0 CD B:CD1001 3.5 35.5 1.0 CG B:GLU92 4.2 27.5 1.0 ND1 B:HIS67 4.3 38.8 1.0 CG B:HIS67 4.3 39.7 1.0 CA B:CYS65 4.8 31.7 1.0 CB B:GLU92 4.9 28.8 1.0 C B:CYS65 5.0 31.2 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