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Fluorine in PDB 5jim: Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)

Protein crystallography data

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos), PDB code: 5jim was solved by A.Begum, J.Zhang, A.Olofsson, P.Andersson, A.E.Sauer-Eriksson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.51 / 1.26
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 43.146, 85.413, 64.121, 90.00, 90.00, 90.00
R / Rfree (%) 13.5 / 15.8

Other elements in 5jim:

The structure of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) (pdb code 5jim). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 34 binding sites of Fluorine where determined in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos), PDB code: 5jim:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 34 in 5jim

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Fluorine binding site 1 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:44.5
occ:0.50
 F8C A:P8S201 0.0 44.5 0.5
C8 A:P8S201 1.3 44.6 0.5
F8A A:P8S201 2.2 45.7 0.5
F8B A:P8S201 2.2 44.5 0.5
C7 A:P8S201 2.3 44.6 0.5
F7B A:P8S201 2.4 44.7 0.5
F4A A:P8S201 2.6 45.9 0.5
F5B A:P8S201 2.9 45.1 0.5
HD22 A:LEU110 3.0 20.4 1.0
F7A A:P8S201 3.3 44.6 0.5
C6 A:P8S201 3.3 44.9 0.5
C5 A:P8S201 3.4 45.5 0.5
C4 A:P8S201 3.5 45.8 0.5
CD2 A:LEU110 3.9 17.0 1.0
F6A A:P8S201 4.0 43.2 0.5
F4B A:P8S201 4.1 45.9 0.5
HD23 A:LEU110 4.1 20.4 1.0
HD21 A:LEU110 4.3 20.4 1.0
F6B A:P8S201 4.4 46.0 0.5
HB2 A:LEU110 4.5 17.1 1.0
F5A A:P8S201 4.7 46.3 0.5
HD13 A:LEU110 4.7 18.5 1.0
C3 A:P8S201 4.7 45.9 0.5
F3B A:P8S201 4.8 45.8 0.5
CG A:LEU110 4.9 14.4 1.0

Fluorine binding site 2 out of 34 in 5jim

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Fluorine binding site 2 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:45.7
occ:0.50
 F8A A:P8S201 0.0 45.7 0.5
C8 A:P8S201 1.3 44.6 0.5
F8B A:P8S201 2.1 44.5 0.5
F8C A:P8S201 2.2 44.5 0.5
C7 A:P8S201 2.3 44.6 0.5
F7A A:P8S201 2.4 44.6 0.5
F7B A:P8S201 3.1 44.7 0.5
C6 A:P8S201 3.5 44.9 0.5
F6A A:P8S201 3.7 43.2 0.5
F4A A:P8S201 4.0 45.9 0.5
C5 A:P8S201 4.4 45.5 0.5
F5B A:P8S201 4.4 45.1 0.5
F4B A:P8S201 4.5 45.9 0.5
F6B A:P8S201 4.5 46.0 0.5
C4 A:P8S201 4.5 45.8 0.5
HD22 A:LEU110 4.6 20.4 1.0

Fluorine binding site 3 out of 34 in 5jim

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Fluorine binding site 3 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:44.5
occ:0.50
 F8B A:P8S201 0.0 44.5 0.5
C8 A:P8S201 1.3 44.6 0.5
F8A A:P8S201 2.1 45.7 0.5
F8C A:P8S201 2.2 44.5 0.5
F4A A:P8S201 2.3 45.9 0.5
C7 A:P8S201 2.4 44.6 0.5
F4B A:P8S201 2.5 45.9 0.5
F6A A:P8S201 2.6 43.2 0.5
C4 A:P8S201 2.7 45.8 0.5
C6 A:P8S201 2.7 44.9 0.5
C5 A:P8S201 3.1 45.5 0.5
F7A A:P8S201 3.1 44.6 0.5
F7B A:P8S201 3.4 44.7 0.5
F5B A:P8S201 3.4 45.1 0.5
F6B A:P8S201 4.0 46.0 0.5
C3 A:P8S201 4.1 45.9 0.5
F5A A:P8S201 4.3 46.3 0.5
F3B A:P8S201 4.5 45.8 0.5
F2B A:P8S201 4.6 47.4 0.5
C2 A:P8S201 4.9 48.1 0.5
F3A A:P8S201 4.9 44.5 0.5
HD22 A:LEU110 5.0 20.4 1.0

Fluorine binding site 4 out of 34 in 5jim

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Fluorine binding site 4 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:44.6
occ:0.50
 F7A A:P8S201 0.0 44.6 0.5
C7 A:P8S201 1.3 44.6 0.5
F7B A:P8S201 2.1 44.7 0.5
C8 A:P8S201 2.3 44.6 0.5
C6 A:P8S201 2.3 44.9 0.5
F8A A:P8S201 2.4 45.7 0.5
F6B A:P8S201 2.6 46.0 0.5
F6A A:P8S201 2.7 43.2 0.5
F8B A:P8S201 3.1 44.5 0.5
F8C A:P8S201 3.3 44.5 0.5
HB3 A:SER117 3.5 20.2 1.0
C5 A:P8S201 3.7 45.5 0.5
F5B A:P8S201 3.9 45.1 0.5
HB2 A:SER117 3.9 20.2 1.0
CB A:SER117 4.2 16.9 1.0
C4 A:P8S201 4.5 45.8 0.5
HD22 A:LEU110 4.5 20.4 1.0
F4B A:P8S201 4.5 45.9 0.5
F5A A:P8S201 4.5 46.3 0.5
F4A A:P8S201 4.6 45.9 0.5
HD23 A:LEU110 4.7 20.4 1.0
HB A:THR119 4.7 18.8 1.0
OG A:SER117 4.8 19.9 1.0
HB3 A:LEU110 4.8 17.1 1.0
HB2 A:LEU110 4.9 17.1 1.0

Fluorine binding site 5 out of 34 in 5jim

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Fluorine binding site 5 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:44.7
occ:0.50
 F7B A:P8S201 0.0 44.7 0.5
C7 A:P8S201 1.3 44.6 0.5
F7A A:P8S201 2.1 44.6 0.5
C8 A:P8S201 2.3 44.6 0.5
C6 A:P8S201 2.3 44.9 0.5
F5B A:P8S201 2.3 45.1 0.5
F8C A:P8S201 2.4 44.5 0.5
HD22 A:LEU110 2.5 20.4 1.0
F6B A:P8S201 2.6 46.0 0.5
C5 A:P8S201 2.8 45.5 0.5
HB2 A:LEU110 2.9 17.1 1.0
HD23 A:LEU110 3.0 20.4 1.0
F8A A:P8S201 3.1 45.7 0.5
HB3 A:LEU110 3.1 17.1 1.0
CD2 A:LEU110 3.2 17.0 1.0
F8B A:P8S201 3.4 44.5 0.5
CB A:LEU110 3.4 14.2 1.0
HB2 A:SER117 3.4 20.2 1.0
F6A A:P8S201 3.5 43.2 0.5
F5A A:P8S201 3.7 46.3 0.5
F4A A:P8S201 3.8 45.9 0.5
CG A:LEU110 3.9 14.4 1.0
C4 A:P8S201 3.9 45.8 0.5
HB3 A:SER117 3.9 20.2 1.0
HD21 A:LEU110 4.0 20.4 1.0
CB A:SER117 4.1 16.9 1.0
HD13 A:LEU110 4.4 18.5 1.0
F4B A:P8S201 4.5 45.9 0.5
HG A:LEU110 4.6 17.3 1.0
H A:LEU110 4.7 15.9 1.0
CD1 A:LEU110 4.7 15.4 1.0
OG A:SER117 4.8 19.9 1.0
CA A:LEU110 4.8 12.9 1.0
N A:LEU110 5.0 13.2 1.0

Fluorine binding site 6 out of 34 in 5jim

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Fluorine binding site 6 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:43.2
occ:0.50
 F6A A:P8S201 0.0 43.2 0.5
C6 A:P8S201 1.3 44.9 0.5
F6B A:P8S201 2.1 46.0 0.5
F4B A:P8S201 2.3 45.9 0.5
C5 A:P8S201 2.3 45.5 0.5
C7 A:P8S201 2.3 44.6 0.5
F8B A:P8S201 2.6 44.5 0.5
F7A A:P8S201 2.7 44.6 0.5
C4 A:P8S201 2.7 45.8 0.5
F5A A:P8S201 2.9 46.3 0.5
C8 A:P8S201 3.0 44.6 0.5
HG21 A:THR119 3.1 21.8 1.0
HG22 A:THR119 3.3 21.8 1.0
F5B A:P8S201 3.4 45.1 0.5
F7B A:P8S201 3.5 44.7 0.5
F4A A:P8S201 3.5 45.9 0.5
CG2 A:THR119 3.7 18.2 1.0
F8A A:P8S201 3.7 45.7 0.5
HB A:THR119 3.9 18.8 1.0
F8C A:P8S201 4.0 44.5 0.5
C3 A:P8S201 4.0 45.9 0.5
F2A A:P8S201 4.1 47.9 0.5
CB A:THR119 4.4 15.7 1.0
F3A A:P8S201 4.4 44.5 0.5
HG23 A:THR119 4.5 21.8 1.0
C2 A:P8S201 4.5 48.1 0.5
F2B A:P8S201 4.5 47.4 0.5
HB3 A:ALA108 4.6 19.6 1.0
HG1 A:THR119 4.9 20.7 1.0

Fluorine binding site 7 out of 34 in 5jim

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Fluorine binding site 7 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:46.0
occ:0.50
 F6B A:P8S201 0.0 46.0 0.5
C6 A:P8S201 1.3 44.9 0.5
F6A A:P8S201 2.1 43.2 0.5
C7 A:P8S201 2.3 44.6 0.5
C5 A:P8S201 2.3 45.5 0.5
F5A A:P8S201 2.4 46.3 0.5
F7A A:P8S201 2.6 44.6 0.5
F7B A:P8S201 2.6 44.7 0.5
F5B A:P8S201 2.9 45.1 0.5
HG22 A:THR119 3.3 21.8 1.0
C4 A:P8S201 3.6 45.8 0.5
C8 A:P8S201 3.7 44.6 0.5
HB2 A:LEU110 3.9 17.1 1.0
HB A:THR119 3.9 18.8 1.0
F4B A:P8S201 3.9 45.9 0.5
HB3 A:SER117 4.0 20.2 1.0
HA A:THR118 4.0 17.7 1.0
F8B A:P8S201 4.0 44.5 0.5
HG21 A:THR119 4.0 21.8 1.0
CG2 A:THR119 4.0 18.2 1.0
HB2 A:SER117 4.1 20.2 1.0
HB3 A:LEU110 4.2 17.1 1.0
HB3 A:ALA108 4.2 19.6 1.0
H A:THR119 4.2 16.9 1.0
O A:SER117 4.2 16.3 1.0
F4A A:P8S201 4.3 45.9 0.5
F8C A:P8S201 4.4 44.5 0.5
H A:LEU110 4.4 15.9 1.0
F3A A:P8S201 4.4 44.5 0.5
N A:THR119 4.4 14.1 1.0
HB1 A:ALA108 4.4 19.6 1.0
CB A:THR119 4.4 15.7 1.0
C A:SER117 4.5 14.2 1.0
CB A:LEU110 4.5 14.2 1.0
CB A:SER117 4.5 16.9 1.0
F8A A:P8S201 4.5 45.7 0.5
HA A:ALA109 4.5 17.6 1.0
O A:ALA108 4.6 14.8 1.0
C A:THR118 4.6 14.4 1.0
CA A:THR118 4.6 14.7 1.0
C3 A:P8S201 4.6 45.9 0.5
N A:THR118 4.7 14.2 1.0
N A:LEU110 4.7 13.2 1.0
CB A:ALA108 4.8 16.3 1.0
F2A A:P8S201 4.8 47.9 0.5
C A:ALA108 4.9 14.2 1.0
HG23 A:THR119 4.9 21.8 1.0
HD22 A:LEU110 4.9 20.4 1.0

Fluorine binding site 8 out of 34 in 5jim

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Fluorine binding site 8 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:45.1
occ:0.50
 F5B A:P8S201 0.0 45.1 0.5
C5 A:P8S201 1.3 45.5 0.5
F5A A:P8S201 2.2 46.3 0.5
C4 A:P8S201 2.3 45.8 0.5
C6 A:P8S201 2.3 44.9 0.5
F7B A:P8S201 2.3 44.7 0.5
F4A A:P8S201 2.4 45.9 0.5
HB2 A:LEU110 2.6 17.1 1.0
C7 A:P8S201 2.6 44.6 0.5
F3A A:P8S201 2.8 44.5 0.5
F8C A:P8S201 2.9 44.5 0.5
F6B A:P8S201 2.9 46.0 0.5
C3 A:P8S201 3.0 45.9 0.5
HD12 A:LEU17 3.1 22.5 1.0
C8 A:P8S201 3.1 44.6 0.5
HD22 A:LEU110 3.2 20.4 1.0
F6A A:P8S201 3.4 43.2 0.5
F4B A:P8S201 3.4 45.9 0.5
F8B A:P8S201 3.4 44.5 0.5
F3B A:P8S201 3.5 45.8 0.5
CB A:LEU110 3.5 14.2 1.0
HD13 A:LEU110 3.6 18.5 1.0
HB3 A:LEU110 3.8 17.1 1.0
F7A A:P8S201 3.9 44.6 0.5
CD2 A:LEU110 4.0 17.0 1.0
CD1 A:LEU17 4.0 18.8 1.0
CG A:LEU110 4.1 14.4 1.0
CD1 A:LEU110 4.3 15.4 1.0
HD11 A:LEU17 4.3 22.5 1.0
HD23 A:LEU110 4.3 20.4 1.0
HD13 A:LEU17 4.4 22.5 1.0
HB2 A:LEU17 4.4 18.3 1.0
F8A A:P8S201 4.4 45.7 0.5
C2 A:P8S201 4.4 48.1 0.5
CA A:LEU110 4.5 12.9 1.0
F2A A:P8S201 4.6 47.9 0.5
HA A:LEU110 4.6 15.5 1.0
N A:LEU110 4.7 13.2 1.0
HD21 A:LEU110 4.7 20.4 1.0
HD12 A:LEU110 4.8 18.5 1.0
H A:LEU110 4.8 15.9 1.0
HB1 A:ALA108 4.8 19.6 1.0
HG A:LEU17 4.9 19.7 1.0
CG A:LEU17 5.0 16.4 1.0
HD11 A:LEU110 5.0 18.5 1.0
F2B A:P8S201 5.0 47.4 0.5

Fluorine binding site 9 out of 34 in 5jim

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Fluorine binding site 9 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:46.3
occ:0.50
 F5A A:P8S201 0.0 46.3 0.5
C5 A:P8S201 1.3 45.5 0.5
F3A A:P8S201 2.0 44.5 0.5
F5B A:P8S201 2.2 45.1 0.5
C6 A:P8S201 2.3 44.9 0.5
C4 A:P8S201 2.3 45.8 0.5
F6B A:P8S201 2.4 46.0 0.5
C3 A:P8S201 2.6 45.9 0.5
HB1 A:ALA108 2.8 19.6 1.0
F6A A:P8S201 2.9 43.2 0.5
F2A A:P8S201 3.0 47.9 0.5
F4B A:P8S201 3.1 45.9 0.5
HB3 A:ALA108 3.3 19.6 1.0
F4A A:P8S201 3.4 45.9 0.5
C2 A:P8S201 3.4 48.1 0.5
CB A:ALA108 3.5 16.3 1.0
C7 A:P8S201 3.6 44.6 0.5
F3B A:P8S201 3.7 45.8 0.5
HD12 A:LEU17 3.7 22.5 1.0
F7B A:P8S201 3.7 44.7 0.5
HB2 A:LEU110 3.8 17.1 1.0
HG22 A:THR119 3.9 21.8 1.0
HB2 A:ALA108 4.1 19.6 1.0
F1B A:P8S201 4.2 52.2 0.5
F2B A:P8S201 4.3 47.4 0.5
F8B A:P8S201 4.3 44.5 0.5
C A:ALA108 4.4 14.2 1.0
C8 A:P8S201 4.4 44.6 0.5
N A:ALA109 4.4 14.5 1.0
C1 A:P8S201 4.5 51.8 0.5
F7A A:P8S201 4.5 44.6 0.5
CD1 A:LEU17 4.5 18.8 1.0
CA A:ALA108 4.6 15.2 1.0
H A:ALA109 4.6 17.4 1.0
HD11 A:LEU17 4.6 22.5 1.0
C A:ALA109 4.6 13.6 1.0
CB A:LEU110 4.6 14.2 1.0
N A:LEU110 4.7 13.2 1.0
F8C A:P8S201 4.7 44.5 0.5
HG21 A:THR119 4.7 21.8 1.0
O A:ALA108 4.7 14.8 1.0
HA A:ALA109 4.7 17.6 1.0
CG2 A:THR119 4.7 18.2 1.0
HG A:LEU17 4.8 19.7 1.0
H A:LEU110 4.8 15.9 1.0
O A:ALA109 4.8 15.7 1.0
HB3 A:LEU110 4.8 17.1 1.0
CA A:ALA109 4.9 14.7 1.0
HA A:ALA108 5.0 18.2 1.0
HB2 A:LEU17 5.0 18.3 1.0

Fluorine binding site 10 out of 34 in 5jim

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Fluorine binding site 10 out of 34 in the Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Transthyretin in Complex with Perfluoroktansulfonsyra (Pfos) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:45.9
occ:0.50
 F4A A:P8S201 0.0 45.9 0.5
C4 A:P8S201 1.3 45.8 0.5
F4B A:P8S201 2.2 45.9 0.5
C3 A:P8S201 2.3 45.9 0.5
F3B A:P8S201 2.3 45.8 0.5
F8B A:P8S201 2.3 44.5 0.5
C5 A:P8S201 2.3 45.5 0.5
F5B A:P8S201 2.4 45.1 0.5
F8C A:P8S201 2.6 44.5 0.5
C8 A:P8S201 2.8 44.6 0.5
F3A A:P8S201 3.1 44.5 0.5
C6 A:P8S201 3.2 44.9 0.5
F5A A:P8S201 3.4 46.3 0.5
C7 A:P8S201 3.4 44.6 0.5
C2 A:P8S201 3.4 48.1 0.5
F2B A:P8S201 3.4 47.4 0.5
F6A A:P8S201 3.5 43.2 0.5
F7B A:P8S201 3.8 44.7 0.5
HD12 A:LEU17 3.8 22.5 1.0
F8A A:P8S201 4.0 45.7 0.5
F2A A:P8S201 4.1 47.9 0.5
HD11 A:LEU17 4.3 22.5 1.0
F6B A:P8S201 4.3 46.0 0.5
CD1 A:LEU17 4.4 18.8 1.0
HD22 A:LEU110 4.6 20.4 1.0
HD13 A:LEU17 4.6 22.5 1.0
C1 A:P8S201 4.6 51.8 0.5
F7A A:P8S201 4.6 44.6 0.5
F1A A:P8S201 4.6 53.1 0.5
HB2 A:LEU110 4.9 17.1 1.0
F1B A:P8S201 4.9 52.2 0.5

Reference:

J.Zhang, A.Begum, K.Brannstrom, C.Grundstrom, I.Iakovleva, A.Olofsson, A.E.Sauer-Eriksson, P.L.Andersson. Structure-Based Virtual Screening Protocol For in Silico Identification of Potential Thyroid Disrupting Chemicals Targeting Transthyretin. Environ. Sci. Technol. V. 50 11984 2016.
ISSN: ISSN 1520-5851
PubMed: 27668830
DOI: 10.1021/ACS.EST.6B02771
Page generated: Thu Aug 1 10:33:37 2024

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