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

The structure of Fragment-Based Design of Novel Estrogen Receptor Ligands, PDB code: 3omp 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)	19.56 / 2.05
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	70.720, 70.720, 109.810, 90.00, 90.00, 120.00
R / Rfree (%)	19.8 / 25.5

The binding sites of Fluorine atom in the Fragment-Based Design of Novel Estrogen Receptor Ligands (pdb code 3omp). 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: 3omp:
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:25.4 occ:1.00 FAC A:W141 0.0 25.4 1.0 CAQ A:W141 1.3 21.9 1.0 FAD A:W141 2.0 19.7 1.0 FAE A:W141 2.3 23.2 1.0 CAL A:W141 2.3 21.4 1.0 CAJ A:W141 2.8 15.1 1.0 NAP A:W141 2.9 17.2 1.0 OAA A:W141 3.3 27.4 1.0 CA A:GLY472 3.3 13.6 1.0 CE A:MET340 3.8 20.1 1.0 CAI A:W141 3.9 12.2 1.0 SD A:MET336 3.9 15.8 1.0 CE A:MET336 3.9 17.0 1.0 C A:GLY472 4.0 14.2 1.0 O A:GLY472 4.1 14.1 1.0 CAK A:W141 4.2 13.9 1.0 CG2 A:ILE376 4.3 15.2 1.0 N A:GLY472 4.6 14.4 1.0 CD1 A:ILE376 4.6 11.8 1.0 CAN A:W141 4.9 8.5 1.0 CG A:MET336 5.0 11.1 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:19.7 occ:1.00 FAD A:W141 0.0 19.7 1.0 CAQ A:W141 1.2 21.9 1.0 FAC A:W141 2.0 25.4 1.0 FAE A:W141 2.3 23.2 1.0 CAL A:W141 2.3 21.4 1.0 NAP A:W141 3.0 17.2 1.0 CAJ A:W141 3.1 15.1 1.0 OAA A:W141 3.2 27.4 1.0 CD1 A:ILE373 3.4 18.6 1.0 CG1 A:ILE373 3.8 16.9 1.0 CG2 A:ILE376 3.9 15.2 1.0 CD1 A:ILE376 4.0 11.8 1.0 CAK A:W141 4.4 13.9 1.0 CB A:ILE376 4.6 13.6 1.0 CA A:GLY472 4.6 13.6 1.0 CAI A:W141 4.6 12.2 1.0 CG1 A:ILE376 4.9 13.9 1.0 ND1 A:HIS475 5.0 24.1 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:23.2 occ:1.00 FAE A:W141 0.0 23.2 1.0 CAQ A:W141 1.5 21.9 1.0 FAD A:W141 2.3 19.7 1.0 FAC A:W141 2.3 25.4 1.0 CAL A:W141 2.4 21.4 1.0 OAA A:W141 2.6 27.4 1.0 O A:GLY472 3.5 14.1 1.0 NAP A:W141 3.7 17.2 1.0 ND1 A:HIS475 3.9 24.1 1.0 CB A:HIS475 4.0 18.4 1.0 CA A:GLY472 4.0 13.6 1.0 C A:GLY472 4.2 14.2 1.0 CG A:HIS475 4.3 19.5 1.0 CD1 A:LEU476 4.3 23.4 1.0 N A:LEU476 4.3 17.8 1.0 CAJ A:W141 4.4 15.1 1.0 CD2 A:LEU476 4.4 20.2 1.0 CB A:LEU476 4.4 19.4 1.0 CE A:MET295 4.5 10.5 1.0 CD1 A:ILE373 4.5 18.6 1.0 CG A:LEU476 4.6 22.7 1.0 CD1 A:ILE376 4.7 11.8 1.0 CG1 A:ILE373 4.7 16.9 1.0 CE A:MET336 4.7 17.0 1.0 CA A:LEU476 4.8 19.2 1.0 CAK A:W141 4.8 13.9 1.0 CE1 A:HIS475 4.9 22.4 1.0 C A:HIS475 5.0 18.9 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:24.6 occ:1.00 FAC B:W141 0.0 24.6 1.0 CAQ B:W141 1.2 23.2 1.0 FAD B:W141 1.9 23.2 1.0 FAE B:W141 2.3 25.6 1.0 CAL B:W141 2.3 22.3 1.0 CAJ B:W141 2.8 15.2 1.0 NAP B:W141 2.8 18.8 1.0 OAA B:W141 3.3 27.1 1.0 CA B:GLY472 3.4 13.6 1.0 CE B:MET340 3.7 21.6 1.0 CAI B:W141 3.7 12.5 1.0 SD B:MET336 4.1 14.6 1.0 CG2 B:ILE376 4.1 14.0 1.0 O B:GLY472 4.1 13.9 1.0 C B:GLY472 4.1 14.7 1.0 CE B:MET336 4.2 15.9 1.0 CAK B:W141 4.2 14.1 1.0 N B:GLY472 4.6 14.7 1.0 CD1 B:ILE376 4.7 13.8 1.0 CAN B:W141 4.8 7.3 1.0 CAO B:W141 5.0 11.4 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:23.2 occ:1.00 FAD B:W141 0.0 23.2 1.0 CAQ B:W141 1.2 23.2 1.0 FAC B:W141 1.9 24.6 1.0 FAE B:W141 2.3 25.6 1.0 CAL B:W141 2.3 22.3 1.0 NAP B:W141 3.0 18.8 1.0 CAJ B:W141 3.1 15.2 1.0 OAA B:W141 3.2 27.1 1.0 CD1 B:ILE373 3.3 18.9 1.0 CG1 B:ILE373 3.8 16.3 1.0 CG2 B:ILE376 4.0 14.0 1.0 CD1 B:ILE376 4.2 13.8 1.0 CAK B:W141 4.3 14.1 1.0 CAI B:W141 4.5 12.5 1.0 CB B:ILE376 4.6 13.2 1.0 CA B:GLY472 4.6 13.6 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:25.6 occ:1.00 FAE B:W141 0.0 25.6 1.0 CAQ B:W141 1.5 23.2 1.0 FAD B:W141 2.3 23.2 1.0 FAC B:W141 2.3 24.6 1.0 CAL B:W141 2.4 22.3 1.0 OAA B:W141 2.6 27.1 1.0 O B:GLY472 3.3 13.9 1.0 NAP B:W141 3.7 18.8 1.0 CA B:GLY472 3.9 13.6 1.0 ND1 B:HIS475 4.0 24.2 1.0 C B:GLY472 4.0 14.7 1.0 CB B:HIS475 4.0 18.5 1.0 CG B:HIS475 4.3 20.5 1.0 CD1 B:LEU476 4.3 25.4 1.0 CD2 B:LEU476 4.4 20.3 1.0 N B:LEU476 4.4 18.2 1.0 CAJ B:W141 4.4 15.2 1.0 CB B:LEU476 4.4 20.4 1.0 CD1 B:ILE373 4.5 18.9 1.0 CE B:MET295 4.6 10.4 1.0 CG B:LEU476 4.6 22.9 1.0 CE B:MET336 4.7 15.9 1.0 CD1 B:ILE376 4.7 13.8 1.0 CG1 B:ILE373 4.7 16.3 1.0 CAK B:W141 4.8 14.1 1.0 CA B:LEU476 4.9 19.6 1.0 CE1 B:HIS475 4.9 22.6 1.0 C B:HIS475 4.9 18.6 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