Fluorine in PDB 6pfm: Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha

The structure of Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha, PDB code: 6pfm was solved by J.R.Kiefer, M.Vinogradova, J.Liang, B.Zhang, X.Wang, J.R.Zbieg, S.S.Labadie, J.Li, N.C.Ray, D.Ortwine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.95 / 2.84
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	144.106, 144.106, 171.064, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 24.9

The binding sites of Fluorine atom in the Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha (pdb code 6pfm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha, PDB code: 6pfm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Gdc-0927 Bound to 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 Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha within 5.0Å range: probe atom residue distance (Å) B Occ D:F601 b:97.0 occ:1.00 F28 D:OGJ601 0.0 97.0 1.0 C27 D:OGJ601 1.4 83.7 1.0 H26 D:OGJ601 2.0 84.9 1.0 H25 D:OGJ601 2.0 85.1 1.0 C25 D:OGJ601 2.3 77.8 1.0 H20 D:OGJ601 2.7 75.7 1.0 H22 D:OGJ601 2.7 77.9 1.0 C24 D:OGJ601 2.9 76.1 1.0 H21 D:OGJ601 3.4 75.7 1.0 C26 D:OGJ601 3.6 76.5 1.0 H23 D:OGJ601 3.8 75.5 1.0 N23 D:OGJ601 4.0 73.0 1.0 H18 D:OGJ601 4.2 66.8 1.0 HD22 D:LEU354 4.3 62.5 1.0 HZ2 D:TRP383 4.3 59.3 1.0 H24 D:OGJ601 4.4 75.5 1.0 C22 D:OGJ601 4.5 66.6 1.0 CZ2 D:TRP383 4.6 57.6 1.0 HD23 D:LEU354 4.6 63.5 1.0 HE1 D:TRP383 4.8 60.5 1.0 CE2 D:TRP383 4.8 57.3 1.0 H17 D:OGJ601 4.9 66.7 1.0 CD2 D:LEU354 4.9 62.5 1.0 NE1 D:TRP383 4.9 59.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Gdc-0927 Bound to 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 Crystal Structure of Gdc-0927 Bound to Estrogen Receptor Alpha within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:0.3 occ:1.00 F28 A:OGJ601 0.0 0.3 1.0 C27 A:OGJ601 1.4 0.0 1.0 H25 A:OGJ601 2.0 0.6 1.0 H26 A:OGJ601 2.0 0.7 1.0 C25 A:OGJ601 2.4 0.1 1.0 H22 A:OGJ601 2.6 0.7 1.0 H20 A:OGJ601 2.9 0.2 1.0 C24 A:OGJ601 3.1 0.3 1.0 C26 A:OGJ601 3.7 0.7 1.0 H21 A:OGJ601 3.7 0.3 1.0 H23 A:OGJ601 3.8 0.9 1.0 H18 A:OGJ601 4.0 90.0 1.0 N23 A:OGJ601 4.1 0.6 1.0 H24 A:OGJ601 4.4 0.0 1.0 C22 A:OGJ601 4.5 89.5 1.0 OD2 A:ASP351 4.6 98.6 1.0 H17 A:OGJ601 4.7 89.5 1.0 HD23 A:LEU354 4.8 0.1 1.0

S.S.Labadie, J.Li, R.A.Blake, J.H.Chang, S.Goodacre, S.J.Hartman, W.Liang, J.R.Kiefer, T.Kleinheinz, T.Lai, J.Liao, D.F.Ortwine, V.Mody, N.C.Ray, F.Roussel, M.Vinogradova, S.K.Yeap, B.Zhang, X.Zheng, J.R.Zbieg, J.Liang, X.Wang. Discovery of A C-8 Hydroxychromene As A Potent Degrader of Estrogen Receptor Alpha with Improved Rat Oral Exposure Over Gdc-0927. Bioorg.Med.Chem.Lett. V. 29 2090 2019.
ISSN: ESSN 1464-3405
PubMed: 31311734
DOI: 10.1016/J.BMCL.2019.07.013