Fluorine in PDB 3omo: Fragment-Based Design of Novel Estrogen Receptor Ligands

The structure of Fragment-Based Design of Novel Estrogen Receptor Ligands, PDB code: 3omo was solved by S.Moecklinghoff, W.A.Van Otterlo, R.Rose, S.Fuchs, M.Dominguez Seoane, H.Waldmann, C.Ottmann, L.Brunsveld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.54 / 2.21
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	70.570, 70.570, 109.990, 90.00, 90.00, 120.00
R / Rfree (%)	20.8 / 26.4

The binding sites of Fluorine atom in the Fragment-Based Design of Novel Estrogen Receptor Ligands (pdb code 3omo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Fragment-Based Design of Novel Estrogen Receptor Ligands, PDB code: 3omo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:24.3 occ:1.00 FAC A:WV71 0.0 24.3 1.0 CAQ A:WV71 1.3 26.9 1.0 CAL A:WV71 2.2 24.2 1.0 FAD A:WV71 2.2 24.3 1.0 FAE A:WV71 2.3 30.9 1.0 OAA A:WV71 2.3 25.0 1.0 NAP A:WV71 3.5 19.4 1.0 O A:GLY472 3.5 13.8 1.0 CD1 A:LEU476 3.7 17.4 1.0 CA A:GLY472 3.8 13.5 1.0 CB A:HIS475 4.0 20.8 1.0 ND1 A:HIS475 4.0 29.4 1.0 C A:GLY472 4.1 14.5 1.0 CAJ A:WV71 4.3 19.4 1.0 CD1 A:ILE373 4.3 13.0 1.0 CG A:HIS475 4.3 23.0 1.0 CD1 A:ILE376 4.3 10.5 1.0 CD2 A:LEU476 4.5 15.9 1.0 CG A:LEU476 4.5 22.9 1.0 CG1 A:ILE373 4.5 14.5 1.0 CE A:MET336 4.6 15.8 1.0 N A:LEU476 4.6 21.5 1.0 CAK A:WV71 4.6 13.0 1.0 CE A:MET295 4.6 6.7 1.0 CB A:LEU476 4.9 22.2 1.0

Fluorine binding site 2 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:24.3 occ:1.00 FAD A:WV71 0.0 24.3 1.0 CAQ A:WV71 1.3 26.9 1.0 FAE A:WV71 2.1 30.9 1.0 FAC A:WV71 2.2 24.3 1.0 CAL A:WV71 2.4 24.2 1.0 CAJ A:WV71 2.9 19.4 1.0 NAP A:WV71 2.9 19.4 1.0 CA A:GLY472 3.1 13.5 1.0 OAA A:WV71 3.3 25.0 1.0 CE A:MET340 3.5 19.9 1.0 CG2 A:ILE376 3.8 13.7 1.0 CAI A:WV71 3.9 16.0 1.0 CE A:MET336 4.0 15.8 1.0 C A:GLY472 4.0 14.5 1.0 SD A:MET336 4.1 17.3 1.0 O A:GLY472 4.1 13.8 1.0 CD1 A:ILE376 4.2 10.5 1.0 N A:GLY472 4.3 14.5 1.0 CAK A:WV71 4.4 13.0 1.0 CB A:ILE376 4.9 11.9 1.0 CG1 A:ILE376 4.9 12.1 1.0

Fluorine binding site 3 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:30.9 occ:1.00 FAE A:WV71 0.0 30.9 1.0 CAQ A:WV71 1.3 26.9 1.0 FAD A:WV71 2.1 24.3 1.0 FAC A:WV71 2.3 24.3 1.0 CAL A:WV71 2.3 24.2 1.0 NAP A:WV71 3.0 19.4 1.0 CAJ A:WV71 3.1 19.4 1.0 OAA A:WV71 3.1 25.0 1.0 CD1 A:ILE373 3.1 13.0 1.0 CG2 A:ILE376 3.5 13.7 1.0 CG1 A:ILE373 3.6 14.5 1.0 CD1 A:ILE376 3.9 10.5 1.0 CB A:ILE376 4.2 11.9 1.0 CAK A:WV71 4.3 13.0 1.0 CAI A:WV71 4.6 16.0 1.0 CG1 A:ILE376 4.6 12.1 1.0 CA A:GLY472 4.6 13.5 1.0 CE1 A:PHE377 4.8 8.5 1.0 CB A:ILE373 5.0 14.1 1.0

Fluorine binding site 4 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:23.2 occ:1.00 FAC B:WV71 0.0 23.2 1.0 CAQ B:WV71 1.4 23.8 1.0 CAL B:WV71 2.2 22.4 1.0 FAE B:WV71 2.3 28.4 1.0 FAD B:WV71 2.3 15.1 1.0 OAA B:WV71 2.3 21.0 1.0 O B:GLY472 3.4 12.8 1.0 NAP B:WV71 3.5 18.5 1.0 CA B:GLY472 3.7 13.2 1.0 CD1 B:LEU476 3.8 20.5 1.0 CB B:HIS475 3.9 21.1 1.0 C B:GLY472 3.9 14.4 1.0 ND1 B:HIS475 4.0 28.1 1.0 CG B:HIS475 4.2 23.7 1.0 CAJ B:WV71 4.3 17.6 1.0 CD1 B:ILE376 4.4 9.9 1.0 CD1 B:ILE373 4.5 15.1 1.0 CD2 B:LEU476 4.5 17.5 1.0 CAK B:WV71 4.5 14.1 1.0 CG B:LEU476 4.6 23.0 1.0 CG1 B:ILE373 4.6 16.1 1.0 N B:LEU476 4.7 21.7 1.0 CE B:MET336 4.7 10.9 1.0 CE B:MET295 4.7 4.8 1.0 CB B:LEU476 4.9 22.8 1.0 N B:GLY472 5.0 13.5 1.0

Fluorine binding site 5 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:15.1 occ:1.00 FAD B:WV71 0.0 15.1 1.0 CAQ B:WV71 1.3 23.8 1.0 FAE B:WV71 2.0 28.4 1.0 FAC B:WV71 2.3 23.2 1.0 CAL B:WV71 2.3 22.4 1.0 CAJ B:WV71 2.8 17.6 1.0 NAP B:WV71 2.8 18.5 1.0 CA B:GLY472 3.3 13.2 1.0 OAA B:WV71 3.3 21.0 1.0 CAI B:WV71 3.7 15.3 1.0 CG2 B:ILE376 3.7 14.9 1.0 CE B:MET340 4.0 21.4 1.0 SD B:MET336 4.2 15.2 1.0 C B:GLY472 4.2 14.4 1.0 CAK B:WV71 4.2 14.1 1.0 CD1 B:ILE376 4.3 9.9 1.0 O B:GLY472 4.3 12.8 1.0 N B:GLY472 4.4 13.5 1.0 CE B:MET336 4.4 10.9 1.0 CB B:ILE376 4.8 11.2 1.0 CAO B:WV71 4.9 12.6 1.0 CG1 B:ILE376 4.9 9.6 1.0

Fluorine binding site 6 out of 6 in the Fragment-Based Design of Novel Estrogen Receptor Ligands


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Fragment-Based Design of Novel Estrogen Receptor Ligands within 5.0Å range: probe atom residue distance (Å) B Occ B:F1 b:28.4 occ:1.00 FAE B:WV71 0.0 28.4 1.0 CAQ B:WV71 1.3 23.8 1.0 FAD B:WV71 2.0 15.1 1.0 CAL B:WV71 2.2 22.4 1.0 FAC B:WV71 2.3 23.2 1.0 NAP B:WV71 3.0 18.5 1.0 OAA B:WV71 3.0 21.0 1.0 CD1 B:ILE373 3.1 15.1 1.0 CAJ B:WV71 3.2 17.6 1.0 CG1 B:ILE373 3.5 16.1 1.0 CG2 B:ILE376 3.6 14.9 1.0 CD1 B:ILE376 3.9 9.9 1.0 CB B:ILE376 4.2 11.2 1.0 CAK B:WV71 4.3 14.1 1.0 CAI B:WV71 4.6 15.3 1.0 CA B:GLY472 4.6 13.2 1.0 CG1 B:ILE376 4.7 9.6 1.0 CE1 B:PHE377 4.8 9.4 1.0 CB B:ILE373 4.9 15.8 1.0

W.A.Van Otterlo, R.Rose, S.Fuchs, T.J.Zimmermann, M.Dominguez Seoane, H.Waldmann, C.Ottmann, L.Brunsveld. Design and Evaluation of Fragment-Like Estrogen Receptor Tetrahydroisoquinoline Ligands From A Scaffold-Detection Approach. J.Med.Chem. V. 54 2005 2011.
ISSN: ISSN 0022-2623
PubMed: 21381753
DOI: 10.1021/JM1011116