Fluorine in PDB 5kd9: Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative, PDB code: 5kd9 was solved by J.C.Nwachukwu, S.Srinivasan, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbogen, K.W.Nettles, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.56 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.951, 81.654, 58.795, 90.00, 110.97, 90.00
R / Rfree (%)	18.4 / 21.3

The structure of Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative (pdb code 5kd9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative, PDB code: 5kd9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:71.2 occ:1.00 F1 B:OBT601 0.0 71.2 1.0 C20 B:OBT601 1.3 69.1 1.0 F2 B:OBT601 2.0 68.8 1.0 F3 B:OBT601 2.0 71.7 1.0 C19 B:OBT601 2.2 63.7 1.0 N01 B:OBT601 3.0 53.9 1.0 C21 B:OBT601 3.2 46.3 1.0 C22 B:OBT601 3.4 43.7 1.0 C26 B:OBT601 4.0 45.9 1.0 CA B:LEU525 4.1 56.0 1.0 N B:LEU525 4.2 54.8 1.0 C23 B:OBT601 4.3 42.7 1.0 CB B:LEU525 4.3 52.6 1.0 CD1 B:LEU525 4.4 49.5 1.0 CE B:MET343 4.4 53.5 1.0 S01 B:OBT601 4.4 40.7 1.0 O B:GLY521 4.5 39.0 1.0 C B:HIS524 4.5 58.2 1.0 CB B:HIS524 4.7 66.0 1.0 O B:HIS524 4.7 60.0 1.0 C25 B:OBT601 4.8 42.3 1.0 O04 B:OBT601 4.9 35.8 1.0 C24 B:OBT601 4.9 43.5 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:68.8 occ:1.00 F2 B:OBT601 0.0 68.8 1.0 C20 B:OBT601 1.3 69.1 1.0 F1 B:OBT601 2.0 71.2 1.0 F3 B:OBT601 2.0 71.7 1.0 C19 B:OBT601 2.3 63.7 1.0 N01 B:OBT601 3.6 53.9 1.0 CB B:HIS524 3.7 66.0 1.0 O B:GLU419 4.1 0.5 1.0 CB B:MET421 4.3 58.6 1.0 N B:MET421 4.3 64.2 1.0 CA B:MET421 4.3 57.0 1.0 C21 B:OBT601 4.4 46.3 1.0 ND1 B:HIS524 4.4 80.0 1.0 O04 B:OBT601 4.4 35.8 1.0 CG B:MET421 4.5 56.6 1.0 CG1 B:VAL418 4.5 0.7 1.0 S01 B:OBT601 4.5 40.7 1.0 C B:HIS524 4.5 58.2 1.0 CG B:HIS524 4.6 74.2 1.0 C B:GLY420 4.7 0.1 1.0 N B:LEU525 4.7 54.8 1.0 O B:HIS524 4.7 60.0 1.0 CA B:HIS524 4.8 59.4 1.0 O B:GLY521 4.8 39.0 1.0 C22 B:OBT601 4.9 43.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative


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 the Er-Alpha Ligand-Binding Domain (Y537S) in Complex with An N-Trifluoroethyl 4-Chlorobenzyl Obhs-N Derivative within 5.0Å range: probe atom residue distance (Å) B Occ B:F601 b:71.7 occ:1.00 F3 B:OBT601 0.0 71.7 1.0 C20 B:OBT601 1.3 69.1 1.0 F2 B:OBT601 2.0 68.8 1.0 F1 B:OBT601 2.0 71.2 1.0 C19 B:OBT601 2.2 63.7 1.0 N01 B:OBT601 2.6 53.9 1.0 C21 B:OBT601 3.3 46.3 1.0 O04 B:OBT601 3.4 35.8 1.0 S01 B:OBT601 3.4 40.7 1.0 C22 B:OBT601 3.5 43.7 1.0 CG B:MET421 3.6 56.6 1.0 SD B:MET421 3.8 80.5 1.0 CE B:MET343 3.9 53.5 1.0 CB B:MET421 4.0 58.6 1.0 SD B:MET343 4.2 88.6 1.0 C11 B:OBT601 4.3 35.5 1.0 C17 B:OBT601 4.4 33.5 1.0 CG1 B:VAL418 4.5 0.7 1.0 C26 B:OBT601 4.5 45.9 1.0 CA B:MET421 4.6 57.0 1.0 O05 B:OBT601 4.6 45.4 1.0 C23 B:OBT601 4.7 42.7 1.0 O03 B:OBT601 5.0 37.5 1.0

S.Srinivasan, J.C.Nwachukwu, N.E.Bruno, V.Dharmarajan, D.Goswami, I.Kastrati, S.Novick, J.Nowak, V.Cavett, H.B.Zhou, N.Boonmuen, Y.Zhao, J.Min, J.Frasor, B.S.Katzenellenbogen, P.R.Griffin, J.A.Katzenellenbogen, K.W.Nettles. Full Antagonism of the Estrogen Receptor Without A Prototypical Ligand Side Chain. Nat. Chem. Biol. V. 13 111 2017.
ISSN: ESSN 1552-4469
PubMed: 27870835
DOI: 10.1038/NCHEMBIO.2236