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Cadmium in PDB 8chm: Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One

Enzymatic activity of Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One

All present enzymatic activity of Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One:
5.2.1.8;

Protein crystallography data

The structure of Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One, PDB code: 8chm 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) 45.65 / 1.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 35.592, 40.081, 91.212, 90, 90, 90
R / Rfree (%) 13 / 14.6

Other elements in 8chm:

The structure of Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One (pdb code 8chm). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium where determined in the Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One, PDB code: 8chm:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 8chm

Go back to Cadmium Binding Sites List in 8chm
Cadmium binding site 1 out of 2 in the Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-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)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:10.9
occ:1.00
 OE2 A:GLU54 2.3 10.0 1.0
CL A:CL210 2.4 18.5 1.0
CL A:CL206 2.5 14.9 1.0
OE1 A:GLU54 2.5 11.2 1.0
CL A:CL209 2.6 30.6 1.0
CD A:GLU54 2.8 10.2 1.0
HA A:PHE48 3.4 8.5 1.0
H A:MET49 3.6 8.9 1.0
HB2 A:MET49 4.1 11.5 1.0
O A:HOH334 4.1 20.9 1.0
N A:MET49 4.2 8.8 1.0
HB3 A:MET49 4.3 11.5 1.0
CG A:GLU54 4.3 10.3 1.0
CA A:PHE48 4.3 8.4 1.0
CB A:MET49 4.6 11.6 1.0
HG3 A:GLU54 4.6 10.2 1.0
O A:LYS47 4.6 9.9 1.0
C A:PHE48 4.7 8.6 1.0
HG2 A:GLU54 4.7 10.1 1.0
HB2 A:PHE48 4.8 8.7 1.0

Cadmium binding site 2 out of 2 in 8chm

Go back to Cadmium Binding Sites List in 8chm
Cadmium binding site 2 out of 2 in the Human FKBP12 in Complex with (1S,5S,6R)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-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)-10-((S)-(3,5-Dichlorophenyl) Sulfinyl)-3-(Pyridin-2-Ylmethyl)-5-Vinyl-3,10- Diazabicyclo[4.3.1]Decan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:12.3
occ:1.00
 HE2 A:HIS94 1.4 10.3 0.0
NE2 A:HIS94 2.3 10.5 1.0
CL A:CL208 2.4 24.2 1.0
O A:HOH421 2.5 16.1 1.0
CL A:CL207 2.5 21.6 1.0
CE1 A:HIS94 3.2 11.4 1.0
HE1 A:HIS94 3.3 11.1 1.0
CD2 A:HIS94 3.3 10.0 1.0
O A:HOH471 3.5 23.2 1.0
HD2 A:HIS94 3.5 9.9 1.0
HG2 A:PRO78 4.0 10.8 1.0
O A:HOH499 4.1 27.8 1.0
O A:HOH361 4.3 29.8 1.0
ND1 A:HIS94 4.4 10.8 1.0
HD2 A:PRO78 4.4 9.6 1.0
CG A:HIS94 4.5 9.5 1.0
O A:HOH478 4.6 32.0 1.0
O A:HOH350 4.7 11.1 1.0
O A:HOH431 4.8 24.2 1.0
CG A:PRO78 4.9 11.5 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 20:23:22 2024

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