Atomistry » Cadmium » PDB 7viq-8hyf » 8chl
Atomistry »
  Cadmium »
    PDB 7viq-8hyf »
      8chl »

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: Thu Jul 10 15:41:36 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy