Fluorine in PDB 6df6: Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB

The structure of Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB, PDB code: 6df6 was solved by J.R.Kiefer, M.Vinogradova, J.Liang, B.Zhang, D.F.Ortwine, K.W.Nettles, J.C.Nwachukwu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 2.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.386, 58.857, 94.046, 79.75, 75.42, 63.10
R / Rfree (%)	21.8 / 27.3

The binding sites of Fluorine atom in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB (pdb code 6df6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB, PDB code: 6df6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:72.7 occ:1.00 F37 A:G8Y601 0.0 72.7 1.0 C36 A:G8Y601 1.4 70.9 1.0 C34 A:G8Y601 2.4 66.3 1.0 C33 A:G8Y601 3.0 64.9 1.0 CD2 A:LEU539 3.5 66.5 1.0 C35 A:G8Y601 3.8 62.0 1.0 OD2 A:ASP351 4.0 49.0 1.0 CG A:ASP351 4.1 48.4 1.0 N32 A:G8Y601 4.1 61.0 1.0 OD1 A:ASP351 4.2 49.1 1.0 O A:VAL533 4.5 85.3 1.0 CB A:ASP351 4.8 48.1 1.0 CG A:LEU539 5.0 66.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:86.9 occ:1.00 F37 B:G8Y601 0.0 86.9 1.0 C36 B:G8Y601 1.4 89.9 1.0 C34 B:G8Y601 2.4 90.4 1.0 C35 B:G8Y601 2.7 88.1 1.0 CD1 B:LEU354 3.1 59.3 1.0 C33 B:G8Y601 3.3 87.4 1.0 C31 B:G8Y601 3.4 76.7 1.0 N32 B:G8Y601 3.4 83.6 1.0 OD1 B:ASP351 3.5 58.4 1.0 C30 B:G8Y601 4.1 71.8 1.0 CB B:PRO535 4.4 0.8 1.0 CD2 B:LEU539 4.4 90.4 1.0 CG B:ASP351 4.6 56.7 1.0 CG B:LEU354 4.6 58.1 1.0 CA B:PRO535 4.9 0.4 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB within 5.0Å range: probe atom residue distance (Å) B Occ C:F601 b:72.8 occ:1.00 F37 C:G8Y601 0.0 72.8 1.0 C36 C:G8Y601 1.4 69.5 1.0 C34 C:G8Y601 2.4 66.4 1.0 C33 C:G8Y601 2.9 64.5 1.0 CD2 C:LEU539 3.4 67.7 1.0 N32 C:G8Y601 3.7 60.3 1.0 OD1 C:ASP351 3.7 52.6 1.0 C35 C:G8Y601 3.7 62.6 1.0 CG C:ASP351 4.0 52.1 1.0 OD2 C:ASP351 4.3 53.5 1.0 CB C:ASP351 4.7 50.7 1.0 CD2 C:LEU354 4.8 51.0 1.0 CG C:LEU539 4.9 67.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB


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 Estrogen Receptor Alpha in Complex with Receptor Degrader 16AB within 5.0Å range: probe atom residue distance (Å) B Occ D:F601 b:82.8 occ:1.00 F37 D:G8Y601 0.0 82.8 1.0 C36 D:G8Y601 1.4 78.3 1.0 C34 D:G8Y601 2.4 75.0 1.0 C33 D:G8Y601 3.5 70.7 1.0 C35 D:G8Y601 3.8 70.5 1.0 O D:PRO535 4.0 0.1 1.0 CB D:LEU539 4.2 96.9 1.0 N32 D:G8Y601 4.4 66.1 1.0 CB D:SER536 4.6 0.4 1.0 O D:VAL534 4.8 0.7 1.0 CD1 D:LEU354 4.8 65.7 1.0 C D:PRO535 4.9 0.9 1.0

B.Zhang, J.R.Kiefer, R.A.Blake, J.H.Chang, S.Hartman, E.R.Ingalla, T.Kleinheinz, V.Mody, M.Nannini, D.F.Ortwine, Y.Ran, A.Sambrone, D.Sampath, M.Vinogradova, Y.Zhong, J.C.Nwachukwu, K.W.Nettles, T.Lai, J.Liao, X.Zheng, H.Chen, X.Wang, J.Liang. Unexpected Equivalent Potency of A Constrained Chromene Enantiomeric Pair Rationalized By Co-Crystal Structures in Complex with Estrogen Receptor Alpha. Bioorg. Med. Chem. Lett. V. 29 905 2019.
ISSN: ESSN 1464-3405
PubMed: 30732944
DOI: 10.1016/J.BMCL.2019.01.036