Fluorine in PDB 7msa: Gdc-9545 in Complex with Estrogen Receptor Alpha

Protein crystallography data

The structure of Gdc-9545 in Complex with Estrogen Receptor Alpha, PDB code: 7msa was solved by J.R.Kiefer, M.Vinogradova, J.Liang, J.R.Zbieg, X.Wang, D.F.Ortwine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.22 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.081, 58.937, 93.551, 86.43, 75.08, 63.25
R / Rfree (%) 19.4 / 24.6

Other elements in 7msa:

The structure of Gdc-9545 in Complex with Estrogen Receptor Alpha also contains other interesting chemical elements:

Iodine (I) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Gdc-9545 in Complex with Estrogen Receptor Alpha (pdb code 7msa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Gdc-9545 in Complex with Estrogen Receptor Alpha, PDB code: 7msa:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 7msa

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Fluorine binding site 1 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:89.2
occ:1.00
 F22 A:ZNM601 0.0 89.2 1.0
C19 A:ZNM601 1.4 82.9 1.0
F23 A:ZNM601 2.2 83.8 1.0
C20 A:ZNM601 2.4 81.9 1.0
C18 A:ZNM601 2.4 73.8 1.0
N17 A:ZNM601 2.9 67.0 1.0
CD1 A:LEU525 3.2 80.5 1.0
CG A:LEU525 3.2 82.4 1.0
C25 A:ZNM601 3.3 71.4 1.0
F40 A:ZNM601 3.3 70.0 1.0
CD2 A:LEU525 3.4 85.6 1.0
C24 A:ZNM601 3.4 70.1 1.0
O21 A:ZNM601 3.6 90.4 1.0
CD1 A:LEU384 3.6 61.4 1.0
C26 A:ZNM601 3.7 73.7 1.0
C15 A:ZNM601 3.8 71.1 1.0
C2 A:ZNM601 4.0 63.0 1.0
CD2 A:LEU384 4.0 59.5 1.0
C29 A:ZNM601 4.0 75.2 1.0
C27 A:ZNM601 4.3 77.0 1.0
C A:GLY521 4.4 69.5 1.0
O A:GLY521 4.4 71.2 1.0
CG A:LEU384 4.4 57.8 1.0
CA A:GLY521 4.4 66.6 1.0
C28 A:ZNM601 4.5 73.5 1.0
CB A:LEU525 4.7 85.7 1.0
F30 A:ZNM601 4.7 80.9 1.0
C4 A:ZNM601 4.8 63.9 1.0
C14 A:ZNM601 4.9 67.1 1.0
N A:MET522 4.9 72.6 1.0

Fluorine binding site 2 out of 10 in 7msa

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Fluorine binding site 2 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:83.8
occ:1.00
 F23 A:ZNM601 0.0 83.8 1.0
C19 A:ZNM601 1.4 82.9 1.0
F22 A:ZNM601 2.2 89.2 1.0
C20 A:ZNM601 2.4 81.9 1.0
C18 A:ZNM601 2.4 73.8 1.0
O21 A:ZNM601 2.8 90.4 1.0
N17 A:ZNM601 3.0 67.0 1.0
C2 A:ZNM601 3.2 63.0 1.0
CA A:GLY521 3.5 66.6 1.0
CG2 A:ILE424 3.7 72.0 1.0
CE A:MET388 3.7 62.2 1.0
C A:GLY521 4.1 69.5 1.0
CD2 A:LEU384 4.2 59.5 1.0
C1 A:ZNM601 4.2 62.8 1.0
CD1 A:ILE424 4.3 75.4 1.0
C4 A:ZNM601 4.3 63.9 1.0
CD1 A:LEU384 4.3 61.4 1.0
O A:GLY521 4.4 71.2 1.0
C15 A:ZNM601 4.4 71.1 1.0
F40 A:ZNM601 4.6 70.0 1.0
CG A:LEU384 4.7 57.8 1.0
N A:GLY521 4.7 63.7 1.0
C24 A:ZNM601 4.7 70.1 1.0
CB A:ILE424 4.8 71.7 1.0
C25 A:ZNM601 4.9 71.4 1.0
CG A:LEU525 4.9 82.4 1.0
SD A:MET421 4.9 85.7 1.0
N A:MET522 5.0 72.6 1.0

Fluorine binding site 3 out of 10 in 7msa

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Fluorine binding site 3 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:80.9
occ:1.00
 F30 A:ZNM601 0.0 80.9 1.0
C29 A:ZNM601 1.4 75.2 1.0
C28 A:ZNM601 2.3 73.5 1.0
C24 A:ZNM601 2.3 70.1 1.0
C15 A:ZNM601 2.8 71.1 1.0
CB A:LEU346 3.1 81.4 1.0
CE A:MET343 3.3 101.5 1.0
C18 A:ZNM601 3.6 73.8 1.0
C25 A:ZNM601 3.6 71.4 1.0
C27 A:ZNM601 3.6 77.0 1.0
SD A:MET343 3.7 102.2 1.0
N17 A:ZNM601 3.7 67.0 1.0
CE A:MET421 3.8 90.8 1.0
CD1 A:LEU346 3.8 80.2 1.0
C14 A:ZNM601 3.9 67.1 1.0
C26 A:ZNM601 4.1 73.7 1.0
C A:LEU346 4.1 81.5 1.0
CG A:LEU346 4.1 82.4 1.0
N A:THR347 4.2 81.3 1.0
CA A:LEU346 4.2 81.6 1.0
N12 A:ZNM601 4.2 63.8 1.0
O A:MET343 4.5 100.0 1.0
O A:LEU346 4.5 83.3 1.0
OG1 A:THR347 4.6 87.5 1.0
CD2 A:LEU525 4.6 85.6 1.0
C19 A:ZNM601 4.6 82.9 1.0
F40 A:ZNM601 4.7 70.0 1.0
F22 A:ZNM601 4.7 89.2 1.0
N31 A:ZNM601 4.7 72.7 1.0
CA A:MET343 4.8 102.7 1.0
CA A:THR347 4.8 81.9 1.0
C20 A:ZNM601 5.0 81.9 1.0
C2 A:ZNM601 5.0 63.0 1.0

Fluorine binding site 4 out of 10 in 7msa

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Fluorine binding site 4 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:90.2
occ:1.00
 F39 A:ZNM601 0.0 90.2 1.0
C38 A:ZNM601 1.4 91.5 1.0
C37 A:ZNM601 2.4 89.4 1.0
C36 A:ZNM601 3.8 82.2 1.0
N34 A:ZNM601 4.4 76.1 1.0
C35 A:ZNM601 4.5 71.9 1.0
OD2 A:ASP351 4.8 92.6 1.0

Fluorine binding site 5 out of 10 in 7msa

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Fluorine binding site 5 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:70.0
occ:1.00
 F40 A:ZNM601 0.0 70.0 1.0
C25 A:ZNM601 1.4 71.4 1.0
C26 A:ZNM601 2.3 73.7 1.0
C24 A:ZNM601 2.3 70.1 1.0
C15 A:ZNM601 2.9 71.1 1.0
C14 A:ZNM601 2.9 67.1 1.0
N17 A:ZNM601 3.0 67.0 1.0
CD1 A:LEU384 3.0 61.4 1.0
C5 A:ZNM601 3.2 62.5 1.0
F22 A:ZNM601 3.3 89.2 1.0
C4 A:ZNM601 3.6 63.9 1.0
C29 A:ZNM601 3.6 75.2 1.0
N12 A:ZNM601 3.6 63.8 1.0
C27 A:ZNM601 3.6 77.0 1.0
CD1 A:LEU387 3.8 65.3 1.0
C2 A:ZNM601 3.8 63.0 1.0
C6 A:ZNM601 3.9 62.2 1.0
C18 A:ZNM601 3.9 73.8 1.0
C28 A:ZNM601 4.1 73.5 1.0
C11 A:ZNM601 4.1 67.1 1.0
C19 A:ZNM601 4.1 82.9 1.0
CZ3 A:TRP383 4.2 67.6 1.0
CB A:ALA350 4.3 67.2 1.0
CG A:LEU384 4.5 57.8 1.0
CH2 A:TRP383 4.6 68.1 1.0
F23 A:ZNM601 4.6 83.8 1.0
F30 A:ZNM601 4.7 80.9 1.0
N31 A:ZNM601 4.7 72.7 1.0
C7 A:ZNM601 4.8 64.0 1.0
CB A:LEU387 4.9 60.3 1.0
CD1 A:LEU525 5.0 80.5 1.0
CG A:LEU387 5.0 62.9 1.0

Fluorine binding site 6 out of 10 in 7msa

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Fluorine binding site 6 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:77.2
occ:1.00
 F22 C:ZNM601 0.0 77.2 1.0
C19 C:ZNM601 1.4 74.6 1.0
F23 C:ZNM601 2.2 75.7 1.0
C20 C:ZNM601 2.4 79.9 1.0
C18 C:ZNM601 2.4 74.3 1.0
N17 C:ZNM601 3.0 70.0 1.0
CD2 C:LEU525 3.2 80.3 1.0
CG C:LEU525 3.3 75.8 1.0
CD1 C:LEU525 3.5 74.6 1.0
C25 C:ZNM601 3.5 71.9 1.0
C24 C:ZNM601 3.6 68.4 1.0
O21 C:ZNM601 3.6 89.6 1.0
CD1 C:LEU384 3.7 55.8 1.0
F40 C:ZNM601 3.7 73.5 1.0
O C:GLY521 3.8 65.9 1.0
C15 C:ZNM601 3.9 68.9 1.0
C2 C:ZNM601 4.0 70.8 1.0
CD2 C:LEU384 4.0 55.3 1.0
C26 C:ZNM601 4.0 68.1 1.0
C29 C:ZNM601 4.1 68.7 1.0
C C:GLY521 4.2 59.9 1.0
CA C:GLY521 4.2 59.8 1.0
C27 C:ZNM601 4.5 73.5 1.0
CG C:LEU384 4.5 52.8 1.0
C28 C:ZNM601 4.5 67.3 1.0
F30 C:ZNM601 4.6 72.3 1.0
CB C:LEU525 4.8 78.5 1.0
C4 C:ZNM601 4.9 70.2 1.0

Fluorine binding site 7 out of 10 in 7msa

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Fluorine binding site 7 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:75.7
occ:1.00
 F23 C:ZNM601 0.0 75.7 1.0
C19 C:ZNM601 1.4 74.6 1.0
F22 C:ZNM601 2.2 77.2 1.0
C20 C:ZNM601 2.4 79.9 1.0
C18 C:ZNM601 2.4 74.3 1.0
O21 C:ZNM601 2.9 89.6 1.0
N17 C:ZNM601 3.0 70.0 1.0
C2 C:ZNM601 3.3 70.8 1.0
CA C:GLY521 3.3 59.8 1.0
CE C:MET388 3.5 51.9 1.0
CG2 C:ILE424 3.8 64.6 1.0
C C:GLY521 4.0 59.9 1.0
O C:GLY521 4.1 65.9 1.0
C1 C:ZNM601 4.1 69.5 1.0
CD2 C:LEU384 4.4 55.3 1.0
C4 C:ZNM601 4.4 70.2 1.0
C15 C:ZNM601 4.4 68.9 1.0
CD1 C:LEU384 4.5 55.8 1.0
N C:GLY521 4.6 60.5 1.0
CG1 C:ILE424 4.7 68.7 1.0
CB C:ILE424 4.7 66.4 1.0
C24 C:ZNM601 4.8 68.4 1.0
CG C:LEU384 4.9 52.8 1.0
F40 C:ZNM601 4.9 73.5 1.0

Fluorine binding site 8 out of 10 in 7msa

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Fluorine binding site 8 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:72.3
occ:1.00
 F30 C:ZNM601 0.0 72.3 1.0
C29 C:ZNM601 1.3 68.7 1.0
C28 C:ZNM601 2.3 67.3 1.0
C24 C:ZNM601 2.3 68.4 1.0
C15 C:ZNM601 2.8 68.9 1.0
CE C:MET343 3.2 89.7 1.0
CB C:LEU346 3.3 73.1 1.0
C18 C:ZNM601 3.4 74.3 1.0
C25 C:ZNM601 3.6 71.9 1.0
C27 C:ZNM601 3.6 73.5 1.0
N17 C:ZNM601 3.7 70.0 1.0
SD C:MET343 3.7 89.8 1.0
CD1 C:LEU346 3.9 73.9 1.0
C14 C:ZNM601 4.0 71.0 1.0
C26 C:ZNM601 4.1 68.1 1.0
CE C:MET421 4.1 82.9 1.0
CG C:LEU346 4.2 74.2 1.0
C C:LEU346 4.3 73.8 1.0
N12 C:ZNM601 4.4 67.6 1.0
CA C:LEU346 4.4 75.1 1.0
N C:THR347 4.4 77.0 1.0
C19 C:ZNM601 4.5 74.6 1.0
CD2 C:LEU525 4.6 80.3 1.0
OG1 C:THR347 4.6 78.0 1.0
F22 C:ZNM601 4.6 77.2 1.0
O C:MET343 4.6 89.4 1.0
F40 C:ZNM601 4.7 73.5 1.0
O C:LEU346 4.7 68.3 1.0
N31 C:ZNM601 4.7 73.5 1.0
C20 C:ZNM601 4.7 79.9 1.0
CA C:MET343 4.8 91.9 1.0
C2 C:ZNM601 5.0 70.8 1.0

Fluorine binding site 9 out of 10 in 7msa

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Fluorine binding site 9 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:97.2
occ:1.00
 F39 C:ZNM601 0.0 97.2 1.0
C38 C:ZNM601 1.4 89.3 1.0
C37 C:ZNM601 2.4 83.5 1.0
OD1 C:ASP351 3.3 85.3 1.0
C36 C:ZNM601 3.5 80.7 1.0
CG C:ASP351 3.6 83.1 1.0
OD2 C:ASP351 3.9 88.5 1.0
N34 C:ZNM601 4.4 75.4 1.0
CB C:ASP351 4.4 79.5 1.0
CD2 C:LEU354 4.8 75.2 1.0
CA C:ASP351 5.0 74.7 1.0

Fluorine binding site 10 out of 10 in 7msa

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Fluorine binding site 10 out of 10 in the Gdc-9545 in Complex with Estrogen Receptor Alpha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Gdc-9545 in Complex with Estrogen Receptor Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F601

b:73.5
occ:1.00
 F40 C:ZNM601 0.0 73.5 1.0
C25 C:ZNM601 1.4 71.9 1.0
C26 C:ZNM601 2.3 68.1 1.0
C24 C:ZNM601 2.3 68.4 1.0
C14 C:ZNM601 2.8 71.0 1.0
C15 C:ZNM601 2.8 68.9 1.0
N17 C:ZNM601 3.0 70.0 1.0
C5 C:ZNM601 3.1 67.0 1.0
CD1 C:LEU384 3.2 55.8 1.0
N12 C:ZNM601 3.4 67.6 1.0
C4 C:ZNM601 3.5 70.2 1.0
C29 C:ZNM601 3.6 68.7 1.0
C27 C:ZNM601 3.6 73.5 1.0
F22 C:ZNM601 3.7 77.2 1.0
C6 C:ZNM601 3.8 66.3 1.0
C2 C:ZNM601 3.8 70.8 1.0
C11 C:ZNM601 3.9 68.2 1.0
CD1 C:LEU387 3.9 55.9 1.0
C18 C:ZNM601 4.0 74.3 1.0
C28 C:ZNM601 4.1 67.3 1.0
CB C:ALA350 4.2 69.0 1.0
C19 C:ZNM601 4.4 74.6 1.0
CZ3 C:TRP383 4.5 59.6 1.0
CG C:LEU384 4.7 52.8 1.0
F30 C:ZNM601 4.7 72.3 1.0
N31 C:ZNM601 4.7 73.5 1.0
C7 C:ZNM601 4.7 64.9 1.0
CB C:LEU387 4.8 54.2 1.0
F23 C:ZNM601 4.9 75.7 1.0
C10 C:ZNM601 4.9 63.3 1.0
CG C:LEU387 5.0 56.2 1.0

Reference:

J.Liang, J.R.Zbieg. Gdc-9545 (Giredestrant): A Potent and Orally Bioavailable Selective Estrogen Receptor Antagonist and Degrader with An Exceptional Preclinical Profile For Er+ Breast Cancer To Be Published.
Page generated: Fri Aug 2 09:47:09 2024

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