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

Protein crystallography data

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

Cadmium Binding Sites:

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 3ovn

Go back to Cadmium Binding Sites List in 3ovn
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 3ovn

Go back to Cadmium Binding Sites List in 3ovn
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 3ovn

Go back to Cadmium Binding Sites List in 3ovn
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 3ovn

Go back to Cadmium Binding Sites List in 3ovn
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

Reference:

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
Page generated: Sat Dec 12 08:22:47 2020

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