Fluorine in PDB 4ymq: X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.96 / 2.00
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.909, 61.909, 156.965, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.9

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist (pdb code 4ymq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:67.8 occ:1.00 F20 A:ZBD603 0.0 67.8 1.0 C16 A:ZBD603 1.4 74.6 1.0 F21 A:ZBD603 2.3 63.0 1.0 F18 A:ZBD603 2.3 82.6 1.0 F19 A:ZBD603 2.3 79.4 1.0 C14 A:ZBD603 2.4 68.8 1.0 C15 A:ZBD603 2.6 66.7 1.0 F22 A:ZBD603 3.0 69.3 1.0 CD2 A:LEU396 3.3 36.7 1.0 C11 A:ZBD603 3.3 62.9 1.0 O17 A:ZBD603 3.5 68.6 1.0 C10 A:ZBD603 3.7 63.8 1.0 CD2 A:HIS479 3.8 42.4 1.0 F23 A:ZBD603 4.0 66.2 1.0 CG A:LEU396 4.3 32.1 1.0 C12 A:ZBD603 4.4 64.3 1.0 NE2 A:HIS479 4.5 44.0 1.0 SG A:CYS393 4.7 41.5 1.0 CG A:HIS479 4.7 33.9 1.0 CH2 A:TRP317 4.8 40.7 1.0 CD1 A:ILE397 4.8 44.1 1.0 CD1 A:ILE400 4.9 38.3 1.0 C9 A:ZBD603 5.0 64.6 1.0

Fluorine binding site 2 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:79.4 occ:1.00 F19 A:ZBD603 0.0 79.4 1.0 C16 A:ZBD603 1.4 74.6 1.0 F18 A:ZBD603 2.3 82.6 1.0 F20 A:ZBD603 2.3 67.8 1.0 C14 A:ZBD603 2.4 68.8 1.0 O17 A:ZBD603 2.5 68.6 1.0 F22 A:ZBD603 3.1 69.3 1.0 C15 A:ZBD603 3.3 66.7 1.0 C11 A:ZBD603 3.6 62.9 1.0 F21 A:ZBD603 3.8 63.0 1.0 CZ3 A:TRP317 4.0 36.8 1.0 CB A:CYS320 4.1 37.6 1.0 C12 A:ZBD603 4.1 64.3 1.0 CE3 A:TRP317 4.2 35.8 1.0 CH2 A:TRP317 4.4 40.7 1.0 CD2 A:HIS479 4.4 42.4 1.0 F23 A:ZBD603 4.5 66.2 1.0 NE2 A:HIS479 4.5 44.0 1.0 OH A:TYR502 4.6 39.3 1.0 C10 A:ZBD603 4.7 63.8 1.0 CD2 A:TRP317 4.8 33.1 1.0 CD1 A:LEU391 4.9 33.8 1.0 CZ2 A:TRP317 4.9 39.2 1.0

Fluorine binding site 3 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:82.6 occ:1.00 F18 A:ZBD603 0.0 82.6 1.0 C16 A:ZBD603 1.4 74.6 1.0 F19 A:ZBD603 2.3 79.4 1.0 F20 A:ZBD603 2.3 67.8 1.0 C14 A:ZBD603 2.4 68.8 1.0 C11 A:ZBD603 2.6 62.9 1.0 C12 A:ZBD603 3.0 64.3 1.0 O17 A:ZBD603 3.2 68.6 1.0 CD1 A:LEU391 3.3 33.8 1.0 C10 A:ZBD603 3.4 63.8 1.0 C15 A:ZBD603 3.7 66.7 1.0 CD1 A:ILE397 3.7 44.1 1.0 F21 A:ZBD603 3.8 63.0 1.0 C13 A:ZBD603 4.0 64.8 1.0 C9 A:ZBD603 4.3 64.6 1.0 F22 A:ZBD603 4.3 69.3 1.0 SG A:CYS393 4.3 41.5 1.0 CB A:CYS320 4.4 37.6 1.0 CG A:LEU391 4.5 32.7 1.0 C8 A:ZBD603 4.6 64.6 1.0 CD2 A:LEU391 4.6 28.9 1.0 SG A:CYS320 4.7 36.2 1.0 F23 A:ZBD603 4.7 66.2 1.0 CG1 A:ILE397 4.9 42.1 1.0 CD2 A:LEU396 4.9 36.7 1.0

Fluorine binding site 4 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:63.0 occ:1.00 F21 A:ZBD603 0.0 63.0 1.0 C15 A:ZBD603 1.4 66.7 1.0 F20 A:ZBD603 2.3 67.8 1.0 F22 A:ZBD603 2.3 69.3 1.0 F23 A:ZBD603 2.3 66.2 1.0 C14 A:ZBD603 2.4 68.8 1.0 C16 A:ZBD603 2.8 74.6 1.0 C10 A:ZBD603 2.9 63.8 1.0 C11 A:ZBD603 3.1 62.9 1.0 CD1 A:ILE400 3.4 38.3 1.0 O17 A:ZBD603 3.6 68.6 1.0 F18 A:ZBD603 3.8 82.6 1.0 F19 A:ZBD603 3.8 79.4 1.0 CD2 A:HIS479 3.9 42.4 1.0 CE A:MET358 3.9 42.0 1.0 CD2 A:LEU396 4.0 36.7 1.0 C9 A:ZBD603 4.2 64.6 1.0 CG A:HIS479 4.3 33.9 1.0 C12 A:ZBD603 4.4 64.3 1.0 CG A:LEU396 4.5 32.1 1.0 CB A:HIS479 4.5 32.4 1.0 NE2 A:HIS479 4.6 44.0 1.0 CD1 A:LEU396 4.8 35.5 1.0 CG1 A:ILE400 4.9 37.0 1.0

Fluorine binding site 5 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:69.3 occ:1.00 F22 A:ZBD603 0.0 69.3 1.0 C15 A:ZBD603 1.4 66.7 1.0 F23 A:ZBD603 2.3 66.2 1.0 F21 A:ZBD603 2.3 63.0 1.0 C14 A:ZBD603 2.4 68.8 1.0 O17 A:ZBD603 2.7 68.6 1.0 C16 A:ZBD603 3.0 74.6 1.0 F20 A:ZBD603 3.0 67.8 1.0 NE2 A:HIS479 3.1 44.0 1.0 CD2 A:HIS479 3.1 42.4 1.0 F19 A:ZBD603 3.1 79.4 1.0 CD2 A:LEU324 3.3 38.8 1.0 CE A:MET358 3.7 42.0 1.0 C11 A:ZBD603 3.7 62.9 1.0 CE1 A:HIS479 3.8 40.0 1.0 CG A:HIS479 3.8 33.9 1.0 ND1 A:HIS479 4.2 39.1 1.0 C10 A:ZBD603 4.3 63.8 1.0 F18 A:ZBD603 4.3 82.6 1.0 CG A:LEU324 4.4 41.2 1.0 CD1 A:LEU324 4.6 38.1 1.0 CB A:LEU324 4.7 31.9 1.0 C12 A:ZBD603 4.8 64.3 1.0 SD A:MET358 4.8 41.1 1.0 CB A:HIS479 4.8 32.4 1.0 OH A:TYR502 4.9 39.3 1.0

Fluorine binding site 6 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range: probe atom residue distance (Å) B Occ A:F603 b:66.2 occ:1.00 F23 A:ZBD603 0.0 66.2 1.0 C15 A:ZBD603 1.4 66.7 1.0 F22 A:ZBD603 2.3 69.3 1.0 F21 A:ZBD603 2.3 63.0 1.0 C14 A:ZBD603 2.4 68.8 1.0 C11 A:ZBD603 2.8 62.9 1.0 O17 A:ZBD603 2.9 68.6 1.0 C10 A:ZBD603 3.0 63.8 1.0 CE A:MET358 3.5 42.0 1.0 C16 A:ZBD603 3.8 74.6 1.0 C12 A:ZBD603 3.9 64.3 1.0 F20 A:ZBD603 4.0 67.8 1.0 CD1 A:LEU324 4.0 38.1 1.0 C9 A:ZBD603 4.1 64.6 1.0 CD2 A:LEU324 4.1 38.8 1.0 CD1 A:ILE400 4.5 38.3 1.0 F19 A:ZBD603 4.5 79.4 1.0 CG A:LEU324 4.6 41.2 1.0 CE A:MET365 4.6 62.4 1.0 SD A:MET358 4.7 41.1 1.0 F18 A:ZBD603 4.7 82.6 1.0 C13 A:ZBD603 4.8 64.8 1.0 CB A:LEU324 4.9 31.9 1.0 C8 A:ZBD603 4.9 64.6 1.0 SD A:MET365 4.9 55.2 1.0

I.Muegge, D.Collin, B.Cook, M.Hill-Drzewi, J.Horan, S.Kugler, M.Labadia, X.Li, L.Smith, Y.Zhang. Discovery of 1,3-Dihydro-2,1,3-Benzothiadiazole 2,2-Dioxide Analogs As New Rorc Modulators. Bioorg.Med.Chem.Lett. V. 25 1892 2015.
ISSN: ESSN 1464-3405
PubMed: 25840886
DOI: 10.1016/J.BMCL.2015.03.042