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Cadmium in PDB 8chl: Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One

Enzymatic activity of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One

All present enzymatic activity of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One:
5.2.1.8;

Protein crystallography data

The structure of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One, PDB code: 8chl was solved by C.Meyners, P.L.Purder, F.Hausch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.32 / 1.40
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 70.582, 70.582, 84.263, 90, 90, 120
R / Rfree (%) 18.8 / 21.3

Other elements in 8chl:

The structure of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One (pdb code 8chl). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One, PDB code: 8chl:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 1 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:23.9
occ:0.50
 HD1 A:HIS25 1.7 25.1 0.0
O A:HOH375 2.1 30.5 1.0
O A:HOH386 2.2 33.0 1.0
OE2 A:GLU102 2.3 24.1 1.0
ND1 A:HIS25 2.4 24.9 1.0
CE1 A:HIS25 3.2 23.8 1.0
HE1 A:HIS25 3.3 24.1 1.0
CD A:GLU102 3.3 22.2 1.0
HB2 A:HIS25 3.4 14.6 1.0
CG A:HIS25 3.5 18.3 1.0
HD23 A:LEU104 3.6 16.9 1.0
OE1 A:GLU102 3.8 24.4 1.0
CB A:HIS25 3.8 14.1 1.0
HB3 A:HIS25 4.0 14.6 1.0
NE2 A:HIS25 4.4 23.1 1.0
HB3 A:GLU102 4.4 14.6 1.0
CD2 A:HIS25 4.5 26.3 1.0
CD2 A:LEU104 4.6 17.7 1.0
HH12 A:ARG71 4.6 39.8 1.0
CG A:GLU102 4.6 17.6 1.0
HD11 A:LEU104 4.7 16.0 1.0
HB2 A:GLU102 4.9 14.6 1.0
HD22 A:LEU104 4.9 17.0 1.0
HD21 A:LEU104 4.9 16.7 1.0
CB A:GLU102 4.9 14.3 1.0
HG2 A:GLU102 5.0 17.6 1.0

Cadmium binding site 2 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 2 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:42.9
occ:0.75
 OD1 A:ASP32 2.3 27.4 1.0
CG A:ASP32 3.4 25.7 1.0
OD2 A:ASP32 4.0 29.5 1.0
HG2 A:GLU31 4.3 17.4 1.0
HA A:ASP32 4.4 20.6 1.0
CB A:ASP32 4.6 23.7 1.0
H A:ASP32 4.8 18.6 1.0
HB3 A:ASP32 4.9 23.2 1.0
CA A:ASP32 4.9 19.6 1.0

Cadmium binding site 3 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 3 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:23.8
occ:0.50
 O A:HOH315 2.2 22.5 1.0
OE1 A:GLU31 2.3 18.9 1.0
O A:HOH384 2.4 39.4 1.0
CD A:GLU31 3.1 18.1 1.0
OE2 A:GLU31 3.2 23.6 1.0
HG21 A:THR96 3.5 12.2 1.0
O A:HOH352 4.0 29.9 1.0
O A:HOH304 4.1 26.4 1.0
O A:HOH394 4.1 23.7 1.0
OG1 A:THR96 4.4 12.7 1.0
CG2 A:THR96 4.4 12.2 1.0
HB A:THR96 4.5 11.8 1.0
CG A:GLU31 4.6 17.9 1.0
CB A:THR96 4.7 11.6 1.0
HG2 A:GLU31 4.8 17.4 1.0
HG1 A:THR96 4.8 12.5 0.0
HG23 A:THR96 4.9 11.9 1.0
HG22 A:THR96 4.9 12.0 1.0

Cadmium binding site 4 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 4 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:22.9
occ:0.50
 OE2 A:GLU61 2.3 20.0 1.0
O A:HOH307 2.3 29.6 1.0
CD A:GLU61 3.1 23.4 1.0
O A:HOH355 3.3 18.5 1.0
OE1 A:GLU61 3.4 22.9 1.0
O A:HOH334 4.1 16.5 1.0
CG A:GLU61 4.4 19.2 1.0
HG3 A:GLU61 4.4 19.0 1.0
HG2 A:GLU61 4.7 18.8 1.0
HE2 A:TYR80 4.9 18.1 1.0

Cadmium binding site 5 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 5 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:17.8
occ:0.50
 OE2 B:GLU5 2.1 20.9 1.0
CD B:GLU5 3.0 21.6 1.0
OE1 B:GLU5 3.3 23.5 1.0
O B:HOH327 4.0 32.1 1.0
CG B:GLU5 4.4 18.3 1.0
HG2 B:GLU5 4.5 18.7 1.0
HG3 B:GLU5 4.6 18.6 1.0
O4 B:SO4206 4.7 24.2 1.0

Cadmium binding site 6 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 6 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:25.6
occ:0.45
 O B:HOH317 2.3 26.4 1.0
OE1 B:GLU31 2.3 21.2 1.0
CD B:GLU31 3.1 19.5 1.0
OE2 B:GLU31 3.2 24.3 1.0
HG21 B:THR96 3.5 14.6 1.0
O B:HOH318 3.8 32.7 1.0
O B:HOH306 4.0 20.4 1.0
O B:HOH384 4.2 27.8 1.0
CG2 B:THR96 4.5 14.8 1.0
CG B:GLU31 4.5 18.0 1.0
OG1 B:THR96 4.6 15.2 1.0
HB B:THR96 4.6 14.3 1.0
O B:HOH386 4.6 33.8 1.0
HG2 B:GLU31 4.7 17.6 1.0
CB B:THR96 4.8 14.0 1.0
HG23 B:THR96 4.9 14.4 1.0

Cadmium binding site 7 out of 7 in 8chl

Go back to Cadmium Binding Sites List in 8chl
Cadmium binding site 7 out of 7 in the Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Human FKBP12 in Complex with (1S,5S,6R)-9-((3,5-Dichlorophenyl) Sulfonyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,9- Diazabicyclo[4.2.1]Nonan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd205

b:23.9
occ:0.75
 OE2 B:GLU54 2.1 37.2 1.0
OE1 A:GLU54 2.2 14.1 1.0
OE1 B:GLU54 2.6 33.4 1.0
CD B:GLU54 2.6 32.9 1.0
OE2 A:GLU54 2.8 24.6 1.0
CD A:GLU54 2.8 20.3 1.0
HB2 B:MET49 2.9 22.5 1.0
SD B:MET49 3.2 35.8 1.0
HG3 B:MET49 3.4 25.5 1.0
H A:MET49 3.4 13.8 1.0
H B:MET49 3.5 18.9 1.0
CG B:MET49 3.6 24.6 1.0
HA A:PHE48 3.7 13.6 1.0
CB B:MET49 3.7 22.1 1.0
HB2 A:MET49 3.7 16.0 1.0
HB3 A:MET49 3.8 15.8 1.0
N B:MET49 4.0 18.2 1.0
N A:MET49 4.1 13.7 1.0
HA B:PHE48 4.1 17.6 1.0
CG B:GLU54 4.1 29.4 1.0
CB A:MET49 4.2 15.7 1.0
CG A:GLU54 4.3 18.4 1.0
HB3 B:MET49 4.4 22.3 1.0
HG2 B:GLU54 4.4 29.6 1.0
HG3 B:GLU54 4.4 29.3 1.0
CA B:MET49 4.5 20.2 1.0
CA A:PHE48 4.5 13.3 1.0
HG2 B:MET49 4.6 25.5 1.0
HG2 A:GLU54 4.6 19.2 1.0
C B:PHE48 4.7 18.4 1.0
C A:PHE48 4.7 13.8 1.0
HG3 A:GLU54 4.8 19.1 1.0
CA A:MET49 4.8 14.1 1.0
HB2 A:PHE48 4.8 13.0 1.0
HE2 A:MET49 4.8 26.3 1.0
CE B:MET49 4.8 38.4 1.0
CA B:PHE48 4.8 16.9 1.0
HB3 B:GLU54 4.9 25.8 1.0

Reference:

P.L.Purder, C.Meyners, W.O.Sugiarto, J.Kolos, F.Lohr, J.Gebel, T.Nehls, V.Dotsch, F.Lermyte, F.Hausch. Deconstructing Protein Binding of Sulfonamides and Sulfonamide Analogues Jacs Au 2023.
ISSN: ESSN 2691-3704
DOI: 10.1021/JACSAU.3C00241
Page generated: Fri Jul 19 20:21:24 2024

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