Fluorine in PDB 7cfo: Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.

The structure of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee., PDB code: 7cfo was solved by M.Watanabe, M.Fujihara, T.Motoyama, M.Kawasaki, S.Yamada, Y.Takamura, S.Ito, M.Makishima, S.Nakano, H.Kakuta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.757, 99.432, 93.598, 90, 98.31, 90
R / Rfree (%)	22.1 / 26.6

The binding sites of Fluorine atom in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. (pdb code 7cfo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee., PDB code: 7cfo:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


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 Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ A:F500 b:111.2 occ:1.00 F2 A:WZ6500 0.0 111.2 1.0 C8 A:WZ6500 1.3 108.4 1.0 F1 A:WZ6500 2.1 115.6 1.0 F A:WZ6500 2.1 91.5 1.0 C A:WZ6500 2.3 113.0 1.0 N1 A:WZ6500 2.7 105.3 1.0 CD2 A:LEU436 2.9 61.2 1.0 CA A:LEU436 3.6 54.1 1.0 N A:WZ6500 3.6 132.1 1.0 C2 A:WZ6500 4.0 114.2 1.0 CG A:LEU436 4.1 62.1 1.0 CB A:LEU436 4.1 59.4 1.0 O A:LEU433 4.1 61.2 1.0 C A:LEU436 4.2 52.9 1.0 C10 A:WZ6500 4.4 137.5 1.0 C1 A:WZ6500 4.5 120.6 1.0 CA A:LEU433 4.5 50.4 1.0 CD1 C:LEU436 4.5 82.7 1.0 N A:LEU436 4.6 53.4 1.0 O A:CYS432 4.6 44.1 1.0 CD2 A:LEU433 4.6 58.7 1.0 N A:PHE437 4.7 50.2 1.0 C9 A:WZ6500 4.8 140.8 1.0 C A:LEU433 4.8 51.3 1.0 O A:LEU436 4.8 53.6 1.0 CD2 A:PHE438 4.9 79.9 1.0 CD2 C:LEU436 5.0 89.3 1.0

Fluorine binding site 2 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


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 Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ A:F500 b:91.5 occ:1.00 F A:WZ6500 0.0 91.5 1.0 C8 A:WZ6500 1.3 108.4 1.0 F2 A:WZ6500 2.1 111.2 1.0 F1 A:WZ6500 2.1 115.6 1.0 C A:WZ6500 2.4 113.0 1.0 N A:WZ6500 3.1 132.1 1.0 C10 A:WZ6500 3.2 137.5 1.0 C9 A:WZ6500 3.4 140.8 1.0 CB A:PHE438 3.5 61.7 1.0 N1 A:WZ6500 3.6 105.3 1.0 CD2 A:PHE438 3.6 79.9 1.0 N A:PHE439 3.7 51.0 1.0 N A:PHE438 3.8 44.9 1.0 C11 A:WZ6500 4.0 131.7 1.0 CA A:PHE438 4.1 54.9 1.0 CG A:PHE438 4.1 69.3 1.0 C18 A:WZ6500 4.3 145.7 1.0 C A:LEU436 4.3 52.9 1.0 CA A:LEU436 4.3 54.1 1.0 C1 A:WZ6500 4.3 120.6 1.0 C A:PHE438 4.3 55.9 1.0 CD2 A:LEU436 4.4 61.2 1.0 O A:LEU436 4.4 53.6 1.0 C20 A:WZ6500 4.5 172.1 1.0 CB A:PHE439 4.5 50.1 1.0 C2 A:WZ6500 4.5 114.2 1.0 CA A:PHE439 4.6 52.4 1.0 N A:PHE437 4.6 50.2 1.0 O2 A:WZ6500 4.7 131.2 1.0 C12 A:WZ6500 4.7 123.2 1.0 CE2 A:PHE438 4.8 71.8 1.0 CB A:LEU436 4.8 59.4 1.0 C13 A:WZ6500 4.9 139.3 1.0 C A:PHE437 5.0 49.3 1.0

Fluorine binding site 3 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


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 Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ A:F500 b:115.6 occ:1.00 F1 A:WZ6500 0.0 115.6 1.0 C8 A:WZ6500 1.3 108.4 1.0 F2 A:WZ6500 2.1 111.2 1.0 F A:WZ6500 2.1 91.5 1.0 C A:WZ6500 2.4 113.0 1.0 CD2 A:PHE438 3.0 79.9 1.0 N1 A:WZ6500 3.2 105.3 1.0 N A:WZ6500 3.4 132.1 1.0 CE2 A:PHE438 3.7 71.8 1.0 CD2 A:LEU433 3.8 58.7 1.0 C10 A:WZ6500 4.0 137.5 1.0 O A:CYS432 4.0 44.1 1.0 CG A:PHE438 4.1 69.3 1.0 C2 A:WZ6500 4.3 114.2 1.0 CA A:LEU433 4.4 50.4 1.0 CB A:PHE438 4.4 61.7 1.0 N A:PHE438 4.4 44.9 1.0 C1 A:WZ6500 4.5 120.6 1.0 CA A:LEU436 4.5 54.1 1.0 N A:PHE437 4.5 50.2 1.0 C A:CYS432 4.6 44.7 1.0 C11 A:WZ6500 4.6 131.7 1.0 C A:LEU436 4.6 52.9 1.0 O2 A:WZ6500 4.7 131.2 1.0 N A:LEU433 4.7 43.2 1.0 CH2 A:TRP305 4.7 52.3 1.0 C9 A:WZ6500 4.8 140.8 1.0 CD2 A:LEU436 4.8 61.2 1.0 O A:LEU433 4.9 61.2 1.0 CA A:PHE438 5.0 54.9 1.0

Fluorine binding site 4 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:65.2 occ:1.00 F2 B:WZ6500 0.0 65.2 1.0 C8 B:WZ6500 1.3 62.4 1.0 F1 B:WZ6500 1.8 58.5 1.0 F B:WZ6500 1.9 60.0 1.0 C B:WZ6500 2.2 70.3 1.0 N B:WZ6500 2.8 76.8 1.0 C10 B:WZ6500 3.0 77.4 1.0 C9 B:WZ6500 3.3 76.5 1.0 N1 B:WZ6500 3.4 70.7 1.0 C11 B:WZ6500 3.7 76.5 1.0 C23 B:WZ6500 3.8 81.5 1.0 CB B:ALA272 3.9 51.0 1.0 C1 B:WZ6500 4.1 78.4 1.0 O2 B:WZ6500 4.2 79.1 1.0 C18 B:WZ6500 4.2 75.2 1.0 CD1 B:ILE268 4.3 67.7 1.0 C2 B:WZ6500 4.4 80.2 1.0 C12 B:WZ6500 4.5 74.7 1.0 C13 B:WZ6500 4.8 72.7 1.0 O3 B:WZ6500 4.9 80.0 1.0 N B:PHE439 4.9 53.1 1.0 C24 B:WZ6500 4.9 80.7 1.0

Fluorine binding site 5 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:60.0 occ:1.00 F B:WZ6500 0.0 60.0 1.0 C8 B:WZ6500 1.3 62.4 1.0 F2 B:WZ6500 1.9 65.2 1.0 F1 B:WZ6500 2.2 58.5 1.0 C B:WZ6500 2.5 70.3 1.0 N1 B:WZ6500 2.9 70.7 1.0 N B:PHE439 3.0 53.1 1.0 CA B:PHE439 3.3 56.6 1.0 CB B:PHE439 3.5 70.3 1.0 N B:WZ6500 3.7 76.8 1.0 C B:PHE438 3.8 54.6 1.0 CB B:PHE438 3.8 59.7 1.0 C2 B:WZ6500 4.2 80.2 1.0 CA B:PHE438 4.4 56.6 1.0 CD1 B:ILE268 4.4 67.7 1.0 C10 B:WZ6500 4.4 77.4 1.0 O B:PHE438 4.5 48.5 1.0 CG B:PHE439 4.5 91.3 1.0 CD1 B:PHE439 4.5 97.7 1.0 C1 B:WZ6500 4.6 78.4 1.0 C23 B:WZ6500 4.7 81.5 1.0 C B:PHE439 4.8 50.3 1.0 C9 B:WZ6500 5.0 76.5 1.0

Fluorine binding site 6 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ B:F500 b:58.5 occ:1.00 F1 B:WZ6500 0.0 58.5 1.0 C8 B:WZ6500 1.3 62.4 1.0 F2 B:WZ6500 1.8 65.2 1.0 F B:WZ6500 2.2 60.0 1.0 C B:WZ6500 2.4 70.3 1.0 C23 B:WZ6500 2.6 81.5 1.0 N B:WZ6500 3.2 76.8 1.0 N1 B:WZ6500 3.3 70.7 1.0 C25 B:WZ6500 3.3 78.3 1.0 O3 B:WZ6500 3.4 80.0 1.0 C10 B:WZ6500 3.5 77.4 1.0 C24 B:WZ6500 3.6 80.7 1.0 O2 B:WZ6500 3.6 79.1 1.0 C11 B:WZ6500 3.8 76.5 1.0 CB B:ALA272 3.8 51.0 1.0 CB B:PHE438 3.8 59.7 1.0 C26 B:WZ6500 4.1 74.6 1.0 C1 B:WZ6500 4.3 78.4 1.0 C2 B:WZ6500 4.4 80.2 1.0 C9 B:WZ6500 4.4 76.5 1.0 N B:PHE439 4.6 53.1 1.0 C12 B:WZ6500 4.7 74.7 1.0 CG B:PHE438 4.7 60.3 1.0 C B:PHE438 4.8 54.6 1.0 CA B:ALA272 4.8 47.8 1.0 CH2 B:TRP305 4.9 39.8 1.0 CA B:PHE438 4.9 56.6 1.0

Fluorine binding site 7 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ C:F500 b:55.6 occ:1.00 F2 C:WZ6500 0.0 55.6 1.0 C8 C:WZ6500 1.4 59.1 1.0 F1 C:WZ6500 2.2 65.4 1.0 F C:WZ6500 2.2 53.6 1.0 C C:WZ6500 2.4 55.0 1.0 CD1 C:ILE442 3.2 124.3 1.0 N C:WZ6500 3.2 54.6 1.0 C10 C:WZ6500 3.4 59.0 1.0 N1 C:WZ6500 3.4 48.5 1.0 CB C:ALA272 3.5 51.2 1.0 OE1 C:GLN275 3.7 69.6 1.0 C11 C:WZ6500 3.8 58.2 1.0 O2 C:WZ6500 3.8 54.6 1.0 C9 C:WZ6500 4.1 63.6 1.0 CB C:PHE438 4.2 58.1 1.0 CA C:ALA272 4.2 53.3 1.0 C1 C:WZ6500 4.4 48.4 1.0 C2 C:WZ6500 4.5 51.5 1.0 CG1 C:ILE442 4.7 121.6 1.0 C23 C:WZ6500 4.7 52.7 1.0 C12 C:WZ6500 4.7 57.9 1.0 C C:PHE438 4.9 58.9 1.0 CD C:GLN275 4.9 74.3 1.0 C18 C:WZ6500 5.0 60.5 1.0

Fluorine binding site 8 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ C:F500 b:53.6 occ:1.00 F C:WZ6500 0.0 53.6 1.0 C8 C:WZ6500 1.3 59.1 1.0 F1 C:WZ6500 2.1 65.4 1.0 F2 C:WZ6500 2.2 55.6 1.0 C C:WZ6500 2.3 55.0 1.0 N1 C:WZ6500 2.7 48.5 1.0 N C:PHE439 2.9 60.1 1.0 C C:PHE438 3.1 58.9 1.0 CB C:PHE438 3.2 58.1 1.0 CD1 C:ILE442 3.3 124.3 1.0 CA C:PHE439 3.4 71.2 1.0 O C:PHE438 3.6 50.0 1.0 N C:WZ6500 3.6 54.6 1.0 CA C:PHE438 3.7 60.0 1.0 CG C:PHE439 3.8 72.9 1.0 CD1 C:PHE439 3.9 78.2 1.0 C2 C:WZ6500 4.0 51.5 1.0 CB C:PHE439 4.1 72.5 1.0 CD2 C:PHE439 4.2 69.6 1.0 C10 C:WZ6500 4.3 59.0 1.0 CE1 C:PHE439 4.3 75.9 1.0 CG1 C:ILE442 4.4 121.6 1.0 C1 C:WZ6500 4.5 48.4 1.0 CG C:PHE438 4.6 54.0 1.0 C C:PHE439 4.6 76.4 1.0 CE2 C:PHE439 4.6 63.8 1.0 CZ C:PHE439 4.7 70.8 1.0 CB C:ILE442 4.8 111.9 1.0 N C:PHE438 4.8 63.9 1.0 C9 C:WZ6500 4.8 63.6 1.0

Fluorine binding site 9 out of 9 in the Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Rxralpha Ligand Binding Domain Complexed with Cbtf-Ee. within 5.0Å range: probe atom residue distance (Å) B Occ C:F500 b:65.4 occ:1.00 F1 C:WZ6500 0.0 65.4 1.0 C8 C:WZ6500 1.3 59.1 1.0 F C:WZ6500 2.1 53.6 1.0 F2 C:WZ6500 2.2 55.6 1.0 C C:WZ6500 2.4 55.0 1.0 N C:WZ6500 3.0 54.6 1.0 C10 C:WZ6500 3.1 59.0 1.0 C9 C:WZ6500 3.1 63.6 1.0 N1 C:WZ6500 3.5 48.5 1.0 CE1 C:PHE439 3.6 75.9 1.0 CD1 C:PHE439 3.7 78.2 1.0 CB C:ALA272 3.8 51.2 1.0 CD1 C:ILE442 4.0 124.3 1.0 C18 C:WZ6500 4.1 60.5 1.0 C11 C:WZ6500 4.1 58.2 1.0 C1 C:WZ6500 4.2 48.4 1.0 CZ C:PHE439 4.2 70.8 1.0 C20 C:WZ6500 4.3 65.2 1.0 CG C:PHE439 4.3 72.9 1.0 C2 C:WZ6500 4.5 51.5 1.0 CA C:PHE439 4.6 71.2 1.0 O2 C:WZ6500 4.7 54.6 1.0 N C:PHE439 4.7 60.1 1.0 CE2 C:PHE439 4.8 63.8 1.0 CD2 C:PHE439 4.8 69.6 1.0 C17 C:WZ6500 4.9 62.7 1.0 CG2 C:ILE268 4.9 86.3 1.0 C12 C:WZ6500 4.9 57.9 1.0 C13 C:WZ6500 4.9 51.5 1.0 CA C:ALA272 5.0 53.3 1.0

M.Watanabe, M.Fujihara, T.Motoyama, M.Kawasaki, S.Yamada, Y.Takamura, S.Ito, M.Makishima, S.Nakano, H.Kakuta. Discovery of A "Gatekeeper" Antagonist That Blocks Entry Pathway to Retinoid X Receptors (Rxrs) Without Allosteric Ligand Inhibition in Permissive Rxr Heterodimers. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 33356247
DOI: 10.1021/ACS.JMEDCHEM.0C01354