Chlorine 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:

Cadmium (Cd) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 8 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 8chm

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Chlorine binding site 1 out of 8 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 Chlorine with other atoms in the Cl 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:Cl201

b:15.1
occ:1.00
 CLAA A:UT6201 0.0 15.1 1.0
CAB A:UT6201 1.7 10.2 1.0
CAH A:UT6201 2.7 10.7 1.0
CAC A:UT6201 2.7 9.8 1.0
HAH A:UT6201 2.8 10.6 1.0
HAC A:UT6201 2.8 9.6 1.0
HAX A:UT6201 3.0 9.8 1.0
CG A:HIS87 3.2 9.5 1.0
CD2 A:HIS87 3.3 10.2 1.0
ND1 A:HIS87 3.4 10.5 1.0
HB3 A:HIS87 3.5 9.8 1.0
HG23 A:ILE90 3.5 11.6 1.0
CAX A:UT6201 3.6 9.9 1.0
NE2 A:HIS87 3.7 10.0 1.0
CE1 A:HIS87 3.7 10.3 1.0
HD2 A:HIS87 3.7 10.1 1.0
HB2 A:HIS87 3.7 9.8 1.0
CB A:HIS87 3.7 10.0 1.0
HG21 A:ILE90 3.7 11.7 1.0
HD1 A:HIS87 3.8 10.4 0.0
HG12 A:ILE91 3.9 10.6 1.0
CAF A:UT6201 3.9 10.7 1.0
CAD A:UT6201 4.0 8.4 1.0
CG2 A:ILE90 4.0 11.8 1.0
NAW A:UT6201 4.1 9.0 1.0
HG22 A:ILE90 4.2 11.7 1.0
HE2 A:HIS87 4.2 9.9 0.0
HH A:TYR82 4.2 8.7 0.0
OH A:TYR82 4.2 8.7 1.0
HE1 A:HIS87 4.2 10.2 1.0
HBB A:UT6201 4.2 8.2 1.0
HG13 A:ILE91 4.3 10.7 1.0
CZ A:TYR82 4.3 7.9 1.0
CAY A:UT6201 4.4 10.5 1.0
HAY A:UT6201 4.5 10.3 1.0
CAE A:UT6201 4.5 9.6 1.0
HE1 A:TYR82 4.5 8.5 1.0
HBE A:UT6201 4.5 10.3 1.0
CE1 A:TYR82 4.5 8.9 1.0
HD11 A:ILE90 4.6 13.3 1.0
CG1 A:ILE91 4.6 10.7 1.0
CE2 A:TYR82 4.9 7.9 1.0

Chlorine binding site 2 out of 8 in 8chm

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Chlorine binding site 2 out of 8 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 Chlorine with other atoms in the Cl 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:Cl201

b:15.1
occ:1.00
 CLAG A:UT6201 0.0 15.1 1.0
CAF A:UT6201 1.7 10.7 1.0
CAH A:UT6201 2.7 10.7 1.0
CAE A:UT6201 2.7 9.6 1.0
HAH A:UT6201 2.8 10.6 1.0
HAE A:UT6201 2.8 9.6 1.0
O A:HOH320 3.1 18.1 1.0
HD11 A:ILE90 3.2 13.3 1.0
HB2 A:ASP37 3.3 12.0 1.0
CG A:ASP37 3.5 14.4 1.0
OD1 A:ASP37 3.5 18.2 1.0
HD13 A:ILE90 3.6 13.2 1.0
OD2 A:ASP37 3.6 16.6 1.0
HBE A:UT6201 3.7 10.3 1.0
HB5 A:UT6201 3.7 10.2 1.0
CD1 A:ILE90 3.7 13.6 1.0
O A:HOH484 3.7 14.4 1.0
HD12 A:ILE90 3.8 13.3 1.0
CB A:ASP37 3.9 11.8 1.0
CBE A:UT6201 3.9 10.3 1.0
CAB A:UT6201 3.9 10.2 1.0
CAD A:UT6201 4.0 8.4 1.0
HB3 A:ASP37 4.3 12.2 1.0
HD1 A:PHE36 4.5 10.9 1.0
O A:HOH344 4.5 30.9 1.0
CAC A:UT6201 4.5 9.8 1.0
HH12 A:ARG42 4.8 12.8 1.0
HG23 A:ILE90 4.8 11.6 1.0
O A:PHE36 4.8 12.5 1.0
HAM A:UT6201 4.8 8.3 1.0
CBD A:UT6201 5.0 9.9 1.0

Chlorine binding site 3 out of 8 in 8chm

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Chlorine binding site 3 out of 8 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl205

b:10.7
occ:1.00
 H A:GLY89 2.3 12.8 1.0
O A:HOH492 2.6 9.6 1.0
HA A:PRO92 2.8 8.2 1.0
HA A:PRO88 3.0 11.8 1.0
N A:GLY89 3.1 12.8 1.0
H A:ILE90 3.3 12.0 1.0
O A:HOH452 3.4 24.0 1.0
HG3 A:PRO92 3.4 9.7 1.0
O A:HOH362 3.6 10.3 1.0
O A:ILE91 3.6 8.6 1.0
CA A:PRO92 3.6 8.0 1.0
C A:ILE91 3.7 8.1 1.0
N A:PRO92 3.7 8.5 1.0
N A:ILE90 3.7 11.8 1.0
CA A:PRO88 3.8 11.8 1.0
CA A:GLY89 3.9 14.0 1.0
H A:ILE91 3.9 9.5 1.0
C A:PRO88 4.0 12.2 1.0
HA2 A:GLY89 4.0 13.6 1.0
N A:ILE91 4.0 9.5 1.0
O A:HIS87 4.0 10.3 1.0
C A:GLY89 4.1 13.2 1.0
CG A:PRO92 4.1 9.9 1.0
HB3 A:PRO92 4.2 9.0 1.0
HD3 A:PRO93 4.2 9.1 1.0
CB A:PRO92 4.2 9.1 1.0
HD3 A:PRO92 4.3 9.4 1.0
C A:ILE90 4.3 10.3 1.0
CD A:PRO92 4.3 9.6 1.0
CA A:ILE91 4.5 9.0 1.0
CA A:ILE90 4.5 11.4 1.0
N A:PRO88 4.6 11.0 1.0
C A:HIS87 4.7 9.7 1.0
HA A:ILE90 4.7 11.3 1.0
HB3 A:PRO88 4.8 13.5 1.0
C A:PRO92 4.8 7.7 1.0
HA3 A:GLY89 4.8 13.7 1.0
HA A:ILE91 4.9 9.0 1.0
O A:ILE90 4.9 10.8 1.0
H A:HIS87 4.9 9.3 1.0
CB A:PRO88 4.9 14.2 1.0
HG2 A:PRO92 5.0 9.6 1.0

Chlorine binding site 4 out of 8 in 8chm

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Chlorine binding site 4 out of 8 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl206

b:14.9
occ:1.00
 CD A:CD203 2.5 10.9 1.0
O A:HOH345 3.1 17.2 1.0
HA A:PHE48 3.1 8.5 1.0
HG22 A:THR21 3.4 12.1 1.0
CL A:CL210 3.4 18.5 1.0
HB2 A:MET49 3.4 11.5 1.0
OE2 A:GLU54 3.7 10.0 1.0
CL A:CL209 3.7 30.6 1.0
H A:MET49 3.7 8.9 1.0
N A:MET49 3.8 8.8 1.0
CA A:PHE48 3.8 8.4 1.0
HG1 A:THR21 3.8 13.1 0.0
C A:PHE48 3.8 8.6 1.0
HB3 A:LYS47 4.0 10.3 1.0
O A:LYS47 4.1 9.9 1.0
N A:PHE48 4.1 8.8 1.0
HE2 A:MET49 4.2 22.8 1.0
C A:LYS47 4.2 9.0 1.0
CG2 A:THR21 4.2 12.3 1.0
CB A:MET49 4.2 11.6 1.0
HB2 A:LYS47 4.3 10.3 1.0
HG21 A:THR21 4.3 12.1 1.0
HB3 A:MET49 4.4 11.5 1.0
CA A:MET49 4.5 9.6 1.0
O A:PHE48 4.5 9.4 1.0
OG1 A:THR21 4.5 13.3 1.0
HA A:MET49 4.6 9.6 1.0
CB A:LYS47 4.6 10.4 1.0
H A:PHE48 4.6 8.8 1.0
CD A:GLU54 4.7 10.2 1.0
HA A:THR21 4.7 10.2 1.0
OE1 A:GLU54 4.8 11.2 1.0
HG23 A:THR21 4.9 12.0 1.0
CB A:THR21 4.9 11.4 1.0

Chlorine binding site 5 out of 8 in 8chm

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Chlorine binding site 5 out of 8 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl207

b:21.6
occ:1.00
 CD A:CD204 2.5 12.3 1.0
O A:HOH478 2.6 32.0 1.0
HE2 A:HIS94 2.9 10.3 0.0
HE1 A:HIS94 3.1 11.1 1.0
O A:HOH471 3.2 23.2 1.0
O A:HOH421 3.4 16.1 1.0
NE2 A:HIS94 3.5 10.5 1.0
CE1 A:HIS94 3.5 11.4 1.0
O A:HOH431 4.3 24.2 1.0
O A:HOH361 4.6 29.8 1.0
CD2 A:HIS94 4.7 10.0 1.0
ND1 A:HIS94 4.8 10.8 1.0
CL A:CL208 4.9 24.2 1.0

Chlorine binding site 6 out of 8 in 8chm

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Chlorine binding site 6 out of 8 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl208

b:24.2
occ:1.00
 CD A:CD204 2.4 12.3 1.0
O A:HOH350 2.8 11.1 1.0
HE2 A:HIS94 2.8 10.3 0.0
NE2 A:HIS94 3.3 10.5 1.0
O A:HOH421 3.3 16.1 1.0
HD2 A:HIS94 3.3 9.9 1.0
O A:HOH499 3.5 27.8 1.0
HG2 A:PRO78 3.6 10.8 1.0
CD2 A:HIS94 3.6 10.0 1.0
O A:HOH441 3.7 20.3 1.0
HD2 A:PRO78 3.7 9.6 1.0
O A:HOH326 3.8 20.2 1.0
HD3 A:PRO78 3.9 9.3 1.0
HG1 A:THR96 3.9 9.8 0.0
OG1 A:THR96 3.9 9.9 1.0
CD A:PRO78 4.1 9.6 1.0
CG A:PRO78 4.2 11.5 1.0
HG3 A:PRO78 4.3 11.0 1.0
O A:HOH508 4.4 54.9 1.0
CE1 A:HIS94 4.5 11.4 1.0
O A:HOH471 4.8 23.2 1.0
CG A:HIS94 4.9 9.5 1.0
HE1 A:HIS94 4.9 11.1 1.0
CL A:CL207 4.9 21.6 1.0
O A:HIS94 4.9 9.0 1.0

Chlorine binding site 7 out of 8 in 8chm

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Chlorine binding site 7 out of 8 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 Chlorine with other atoms in the Cl binding site number 7 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:Cl209

b:30.6
occ:1.00
 CD A:CD203 2.6 10.9 1.0
HB3 A:MET49 3.0 11.5 1.0
HB2 A:MET49 3.1 11.5 1.0
HG3 A:LYS52 3.1 15.1 1.0
HZ2 A:LYS52 3.2 28.0 1.0
O A:HOH334 3.3 20.9 1.0
OE2 A:GLU54 3.5 10.0 1.0
CB A:MET49 3.5 11.6 1.0
OE1 A:GLU54 3.5 11.2 1.0
HE2 A:MET49 3.6 22.8 1.0
CL A:CL206 3.7 14.9 1.0
CD A:GLU54 3.8 10.2 1.0
HZ1 A:LYS52 3.8 27.7 1.0
NZ A:LYS52 3.9 29.2 1.0
CG A:LYS52 4.0 16.1 1.0
H A:MET49 4.0 8.9 1.0
SD A:MET49 4.2 19.5 1.0
CE A:MET49 4.3 23.6 1.0
CG A:MET49 4.4 14.1 1.0
HB2 A:LYS52 4.4 11.5 1.0
HD2 A:LYS52 4.5 19.7 1.0
HB3 A:LYS52 4.5 11.6 1.0
HZ3 A:LYS52 4.5 28.0 1.0
N A:MET49 4.5 8.8 1.0
HG2 A:LYS52 4.6 14.9 1.0
CB A:LYS52 4.6 11.2 1.0
CA A:MET49 4.6 9.6 1.0
HE3 A:MET49 4.7 22.8 1.0
CD A:LYS52 4.7 20.2 1.0
HG2 A:MET49 4.9 13.7 1.0
CE A:LYS52 4.9 24.1 1.0
CL A:CL210 4.9 18.5 1.0

Chlorine binding site 8 out of 8 in 8chm

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Chlorine binding site 8 out of 8 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 Chlorine with other atoms in the Cl binding site number 8 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:Cl210

b:18.5
occ:1.00
 CD A:CD203 2.4 10.9 1.0
O A:LYS47 2.9 9.9 1.0
HA A:PHE48 2.9 8.5 1.0
OE2 A:GLU54 3.1 10.0 1.0
OE1 A:GLU54 3.3 11.2 1.0
CD A:GLU54 3.4 10.2 1.0
CL A:CL206 3.4 14.9 1.0
CA A:PHE48 3.9 8.4 1.0
C A:LYS47 3.9 9.0 1.0
HB3 A:PHE48 4.1 8.7 1.0
O A:HOH373 4.2 13.5 1.0
HG3 A:GLU54 4.3 10.2 1.0
HB2 A:PHE48 4.3 8.7 1.0
N A:PHE48 4.3 8.8 1.0
CB A:PHE48 4.4 8.9 1.0
H A:MET49 4.4 8.9 1.0
CG A:GLU54 4.5 10.3 1.0
HB2 A:LYS47 4.7 10.3 1.0
C A:PHE48 4.9 8.6 1.0
CL A:CL209 4.9 30.6 1.0
N A:MET49 5.0 8.8 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: Tue Jul 30 07:55:34 2024

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