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:
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
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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
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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
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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
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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
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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
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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
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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
|