Fluorine in PDB 7ymk: Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide

The structure of Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide, PDB code: 7ymk was solved by J.Min, H.B.Hu, Y.Yang, C.E.Dong, H.B.Zhou, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.78 / 2.25
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.481, 101.48, 195.807, 90, 90, 90
R / Rfree (%)	19.4 / 25.3

The binding sites of Fluorine atom in the Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide (pdb code 7ymk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide, PDB code: 7ymk:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:82.3 occ:1.00 FBB B:IX0601 0.0 82.3 1.0 CAZ B:IX0601 1.3 75.2 1.0 FBC B:IX0601 2.1 73.8 1.0 FBA B:IX0601 2.2 94.8 1.0 CAY B:IX0601 2.4 69.5 1.0 NAX B:IX0601 2.9 61.9 1.0 CE B:MET421 3.0 54.4 1.0 CBE B:IX0601 3.5 66.4 1.0 CBD B:IX0601 3.5 63.8 1.0 SD B:MET343 3.9 70.5 1.0 OAV B:IX0601 4.0 57.1 1.0 SAU B:IX0601 4.0 56.5 1.0 CG1 B:VAL418 4.0 98.3 1.0 CB B:MET421 4.1 58.8 1.0 CG B:MET421 4.3 59.8 1.0 SD B:MET421 4.4 54.5 1.0 CE B:MET343 4.5 65.7 1.0 CAN B:IX0601 4.6 51.3 1.0 CA B:MET421 4.7 64.8 1.0 CBF B:IX0601 4.7 66.0 1.0 CB B:VAL418 4.7 96.6 1.0 CBI B:IX0601 4.7 64.5 1.0 O B:GLU419 4.8 81.5 1.0

Fluorine binding site 2 out of 3 in the Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:73.8 occ:1.00 FBC B:IX0601 0.0 73.8 1.0 CAZ B:IX0601 1.2 75.2 1.0 FBB B:IX0601 2.1 82.3 1.0 FBA B:IX0601 2.1 94.8 1.0 CAY B:IX0601 2.2 69.5 1.0 O B:GLU419 3.4 81.5 1.0 NAX B:IX0601 3.5 61.9 1.0 CB B:HIS524 3.5 68.2 1.0 O B:HIS524 3.9 93.1 1.0 C B:HIS524 4.0 86.7 1.0 CBD B:IX0601 4.2 63.8 1.0 CG1 B:VAL418 4.3 98.3 1.0 N B:MET421 4.3 70.1 1.0 CA B:MET421 4.4 64.8 1.0 CA B:HIS524 4.4 72.3 1.0 CB B:MET421 4.4 58.8 1.0 N B:LEU525 4.4 91.4 1.0 C B:GLY420 4.5 75.0 1.0 CG B:HIS524 4.6 72.3 1.0 OAV B:IX0601 4.6 57.1 1.0 C B:GLU419 4.6 78.3 1.0 O B:GLY420 4.6 65.3 1.0 SAU B:IX0601 4.6 56.5 1.0 CBE B:IX0601 4.7 66.4 1.0 O B:GLY521 4.7 55.1 1.0 CE B:MET421 4.8 54.4 1.0

Fluorine binding site 3 out of 3 in the Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Estrogen Receptor Alpha Ligand Binding Domain C381S C417S Y537S Mutant in Complex with An Covalent Selective Estrogen Receptor Degrader 29C and Grip Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:94.8 occ:1.00 FBA B:IX0601 0.0 94.8 1.0 CAZ B:IX0601 1.4 75.2 1.0 FBC B:IX0601 2.1 73.8 1.0 FBB B:IX0601 2.2 82.3 1.0 CAY B:IX0601 2.4 69.5 1.0 NAX B:IX0601 2.9 61.9 1.0 CBD B:IX0601 2.9 63.8 1.0 CBE B:IX0601 3.1 66.4 1.0 CBI B:IX0601 3.7 64.5 1.0 N B:LEU525 3.7 91.4 1.0 CA B:LEU525 3.7 85.9 1.0 C B:HIS524 3.9 86.7 1.0 CBF B:IX0601 3.9 66.0 1.0 CB B:LEU525 3.9 88.9 1.0 CD1 B:LEU525 4.0 97.5 1.0 O B:HIS524 4.0 93.1 1.0 O B:GLY521 4.0 55.1 1.0 CBH B:IX0601 4.5 60.7 1.0 SAU B:IX0601 4.5 56.5 1.0 CB B:HIS524 4.5 68.2 1.0 CE B:MET343 4.5 65.7 1.0 CBG B:IX0601 4.6 60.7 1.0 CG B:LEU525 4.6 95.0 1.0 SD B:MET343 4.8 70.5 1.0 CA B:HIS524 4.8 72.3 1.0

Y.Wang, J.Min, X.Deng, T.Feng, H.Hu, X.Guo, Y.Cheng, B.Xie, Y.Yang, C.C.Chen, R.T.Guo, C.Dong, H.B.Zhou. Discovery of Novel Covalent Selective Estrogen Receptor Degraders Against Endocrine-Resistant Breast Cancer Acta Pharm Sin B 2023.
ISSN: ESSN 2211-3843
DOI: 10.1016/J.APSB.2023.05.005