Chlorine in PDB 8fb1: Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket, PDB code: 8fb1 was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.78 / 2.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.16, 96.486, 56.797, 90, 91.3, 90
R / Rfree (%)	20.6 / 25.3

The structure of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket also contains other interesting chemical elements:

Fluorine

(F)

19 atoms

The binding sites of Chlorine atom in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket (pdb code 8fb1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket, PDB code: 8fb1:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl602 b:31.7 occ:1.00 CL A:4Y5602 0.0 31.7 1.0 C13 A:4Y5602 1.7 27.1 1.0 C12 A:4Y5602 2.7 28.2 1.0 C8 A:4Y5602 2.7 29.7 1.0 C7 A:4Y5602 3.0 30.4 1.0 N1 A:4Y5602 3.2 30.1 1.0 N A:4Y5602 3.3 28.4 1.0 CB A:LEU324 3.5 17.0 1.0 C A:LEU324 3.5 17.1 1.0 CE A:MET358 3.5 18.5 1.0 N A:THR325 3.6 17.4 1.0 O A:LEU324 3.7 19.2 1.0 O A:4Y5602 3.7 33.0 1.0 CG1 A:ILE328 3.9 17.8 1.0 CA A:THR325 4.0 18.5 1.0 C11 A:4Y5602 4.0 28.3 1.0 C9 A:4Y5602 4.1 29.5 1.0 CA A:LEU324 4.2 16.6 1.0 C6 A:4Y5602 4.2 28.5 1.0 C3 A:4Y5602 4.2 27.5 1.0 OG1 A:THR325 4.3 18.0 1.0 O A:ALA321 4.5 18.7 1.0 C10 A:4Y5602 4.6 30.2 1.0 CD1 A:LEU483 4.6 17.6 1.0 C20 A:4Y5602 4.7 28.7 1.0 CB A:ILE328 4.7 17.1 1.0 CG A:LEU324 4.8 16.4 1.0 C4 A:4Y5602 4.8 26.1 1.0 CB A:THR325 4.8 17.9 1.0 CD1 A:ILE328 4.9 18.0 1.0 CD1 A:LEU324 4.9 16.2 1.0 C15 A:4Y5602 5.0 28.7 1.0

Chlorine binding site 2 out of 3 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl603 b:76.7 occ:1.00 CL A:4Y5603 0.0 76.7 1.0 C13 A:4Y5603 1.7 71.5 1.0 C12 A:4Y5603 2.7 70.1 1.0 C8 A:4Y5603 2.8 69.5 1.0 C7 A:4Y5603 3.1 65.6 1.0 O A:4Y5603 3.5 67.2 1.0 N1 A:4Y5603 3.6 60.2 1.0 CE1 B:HIS451 3.9 29.8 1.0 N A:4Y5603 4.0 58.6 1.0 C11 A:4Y5603 4.1 71.4 1.0 NE2 B:HIS451 4.1 29.3 1.0 C9 A:4Y5603 4.1 74.2 1.0 CD2 B:LEU463 4.3 28.4 1.0 CD1 B:LEU463 4.4 29.0 1.0 CB B:LEU463 4.4 27.0 1.0 CD1 A:LEU267 4.6 22.7 1.0 CG B:LEU463 4.6 28.8 1.0 C10 A:4Y5603 4.6 74.6 1.0 C3 A:4Y5603 4.6 56.8 1.0

Chlorine binding site 3 out of 3 in the Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Retenoid-Related Orphan Receptor-Gamma (RORC2) Ligand-Binding Domain in Complex with Compound 6A Andindazole Acid Bound in H12- Pocket within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl602 b:31.5 occ:1.00 CL B:4Y5602 0.0 31.5 1.0 C13 B:4Y5602 1.7 29.5 1.0 C12 B:4Y5602 2.7 31.4 1.0 C8 B:4Y5602 2.7 30.2 1.0 C7 B:4Y5602 3.0 30.6 1.0 N1 B:4Y5602 3.3 29.3 1.0 N B:4Y5602 3.3 28.1 1.0 N B:THR325 3.6 18.5 1.0 CB B:LEU324 3.6 18.3 1.0 C B:LEU324 3.6 18.4 1.0 O B:LEU324 3.7 17.7 1.0 O B:4Y5602 3.7 34.8 1.0 CE B:MET358 3.8 20.1 1.0 CA B:THR325 3.9 20.7 1.0 CG2 B:THR325 3.9 21.4 1.0 CG1 B:ILE328 3.9 15.1 1.0 C11 B:4Y5602 4.0 33.6 1.0 C9 B:4Y5602 4.1 32.2 1.0 C6 B:4Y5602 4.2 28.9 1.0 C3 B:4Y5602 4.3 29.2 1.0 CA B:LEU324 4.3 17.7 1.0 O B:ALA321 4.5 20.5 1.0 CB B:THR325 4.5 21.2 1.0 C10 B:4Y5602 4.6 32.4 1.0 CD1 B:LEU483 4.7 18.0 1.0 C20 B:4Y5602 4.7 30.2 1.0 C4 B:4Y5602 4.8 28.9 1.0 CB B:ILE328 4.8 15.7 1.0 CG B:LEU324 4.8 17.8 1.0 CD1 B:ILE328 4.9 15.3 1.0 CD1 B:LEU324 5.0 18.9 1.0

M.E.Schnute, J.I.Trujillo, K.L.Lee, R.Unwalla, F.F.Vajdos, B.Kauppi, P.Nuhant, A.C.Flick, K.K.Crouse, Y.Zhao, A.Samuel, V.Lombardo, A.P.Taylor, A.L.Brault, J.D.Knafels, M.L.Vazquez, G.Berstein. Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists. Acs Med.Chem.Lett. V. 14 191 2023.
ISSN: ISSN 1948-5875
PubMed: 36793423
DOI: 10.1021/ACSMEDCHEMLETT.2C00500