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

The structure of Fragment-Based Design of Novel Estrogen Receptor Ligands, PDB code: 3omq 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)	19.55 / 1.97
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	70.590, 70.590, 110.090, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 26

The binding sites of Fluorine atom in the Fragment-Based Design of Novel Estrogen Receptor Ligands (pdb code 3omq). 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: 3omq:
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:26.9 occ:1.00 FAK A:W231 0.0 26.9 1.0 CAJ A:W231 1.4 21.7 1.0 FAM A:W231 2.2 23.0 1.0 FAL A:W231 2.3 23.4 1.0 SAR A:W231 2.4 19.9 1.0 OAQ A:W231 2.6 15.3 1.0 OAP A:W231 2.9 19.8 1.0 ND1 A:HIS475 3.7 27.2 1.0 CD1 A:ILE373 3.7 25.2 1.0 CG1 A:ILE373 3.7 19.6 1.0 NAN A:W231 3.9 19.7 1.0 CG A:HIS475 4.0 21.8 1.0 CB A:HIS475 4.0 20.5 1.0 CD1 A:ILE376 4.1 14.9 1.0 O A:GLY472 4.2 15.8 1.0 CE A:MET295 4.3 13.0 1.0 CE1 A:HIS475 4.4 24.4 1.0 CA A:GLY472 4.5 15.5 1.0 CAI A:W231 4.5 18.1 1.0 CAF A:W231 4.6 14.8 1.0 C A:GLY472 4.8 16.5 1.0 CD2 A:HIS475 4.9 21.4 1.0 SD A:MET295 4.9 17.8 1.0 CD1 A:LEU476 4.9 25.8 1.0 N A:LEU476 4.9 19.9 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:23.4 occ:1.00 FAL A:W231 0.0 23.4 1.0 CAJ A:W231 1.3 21.7 1.0 FAM A:W231 2.2 23.0 1.0 FAK A:W231 2.3 26.9 1.0 SAR A:W231 2.5 19.9 1.0 NAN A:W231 3.0 19.7 1.0 CAF A:W231 3.0 14.8 1.0 OAP A:W231 3.0 19.8 1.0 CD1 A:ILE373 3.3 25.2 1.0 CD1 A:LEU298 3.5 12.9 1.0 OAQ A:W231 3.6 15.3 1.0 CAI A:W231 3.8 18.1 1.0 CE A:MET295 3.9 13.0 1.0 CB A:LEU298 4.2 10.9 1.0 CG1 A:ILE373 4.2 19.6 1.0 SD A:MET295 4.3 17.8 1.0 CG A:LEU298 4.5 11.2 1.0 CAB A:W231 4.6 14.3 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:23.0 occ:1.00 FAM A:W231 0.0 23.0 1.0 CAJ A:W231 1.3 21.7 1.0 FAL A:W231 2.2 23.4 1.0 FAK A:W231 2.2 26.9 1.0 SAR A:W231 2.4 19.9 1.0 OAQ A:W231 2.7 15.3 1.0 CAI A:W231 3.0 18.1 1.0 NAN A:W231 3.0 19.7 1.0 CD1 A:ILE373 3.1 25.2 1.0 CG1 A:ILE373 3.7 19.6 1.0 OAP A:W231 3.8 19.8 1.0 CAF A:W231 3.8 14.8 1.0 CG2 A:ILE376 3.9 16.2 1.0 CE1 A:PHE377 4.3 11.0 1.0 CD1 A:ILE376 4.3 14.9 1.0 CB A:ILE376 4.5 14.8 1.0 CAD A:W231 4.6 18.0 1.0 CD1 A:PHE377 4.8 12.2 1.0 CD1 A:LEU298 4.8 12.9 1.0 CB A:ILE373 4.9 18.3 1.0 CG2 A:ILE373 5.0 17.5 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:23.8 occ:1.00 FAK B:W231 0.0 23.8 1.0 CAJ B:W231 1.3 20.9 1.0 FAM B:W231 2.2 22.9 1.0 FAL B:W231 2.3 21.6 1.0 SAR B:W231 2.4 20.8 1.0 OAQ B:W231 2.7 16.5 1.0 OAP B:W231 2.9 18.2 1.0 CD1 B:ILE373 3.6 24.9 1.0 CG1 B:ILE373 3.6 20.2 1.0 NAN B:W231 3.9 20.2 1.0 ND1 B:HIS475 3.9 26.5 1.0 CG B:HIS475 4.0 22.4 1.0 CB B:HIS475 4.1 20.4 1.0 CD1 B:ILE376 4.1 15.3 1.0 O B:GLY472 4.3 14.8 1.0 CE B:MET295 4.3 13.5 1.0 CA B:GLY472 4.4 15.1 1.0 CAI B:W231 4.5 18.0 1.0 CE1 B:HIS475 4.5 25.2 1.0 CAF B:W231 4.6 14.4 1.0 CD2 B:HIS475 4.7 22.8 1.0 C B:GLY472 4.8 16.0 1.0 CG2 B:ILE376 4.9 16.6 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:21.6 occ:1.00 FAL B:W231 0.0 21.6 1.0 CAJ B:W231 1.3 20.9 1.0 FAM B:W231 2.1 22.9 1.0 FAK B:W231 2.3 23.8 1.0 SAR B:W231 2.5 20.8 1.0 CAF B:W231 3.1 14.4 1.0 OAP B:W231 3.1 18.2 1.0 NAN B:W231 3.1 20.2 1.0 CD1 B:ILE373 3.3 24.9 1.0 CD1 B:LEU298 3.5 11.9 1.0 OAQ B:W231 3.7 16.5 1.0 CE B:MET295 3.8 13.5 1.0 CAI B:W231 3.9 18.0 1.0 CB B:LEU298 4.1 10.7 1.0 CG1 B:ILE373 4.2 20.2 1.0 SD B:MET295 4.3 16.7 1.0 CG B:LEU298 4.4 10.1 1.0 CAB B:W231 4.6 14.6 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:22.9 occ:1.00 FAM B:W231 0.0 22.9 1.0 CAJ B:W231 1.3 20.9 1.0 FAL B:W231 2.1 21.6 1.0 FAK B:W231 2.2 23.8 1.0 SAR B:W231 2.5 20.8 1.0 OAQ B:W231 2.8 16.5 1.0 NAN B:W231 3.1 20.2 1.0 CAI B:W231 3.1 18.0 1.0 CD1 B:ILE373 3.1 24.9 1.0 CG1 B:ILE373 3.6 20.2 1.0 OAP B:W231 3.8 18.2 1.0 CAF B:W231 3.8 14.4 1.0 CG2 B:ILE376 3.9 16.6 1.0 CE1 B:PHE377 4.1 10.7 1.0 CD1 B:ILE376 4.5 15.3 1.0 CB B:ILE376 4.5 14.1 1.0 CD1 B:PHE377 4.6 12.1 1.0 CAD B:W231 4.6 16.9 1.0 CD1 B:LEU298 4.6 11.9 1.0 CB B:ILE373 4.9 17.6 1.0 CG2 B:ILE373 5.0 16.6 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