Fluorine in PDB 6l88: Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone

The structure of Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone, PDB code: 6l88 was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 3.00
Space group	P 21 3
Cell size a, b, c (Å), α, β, γ (°)	160.888, 160.888, 160.888, 90.00, 90.00, 90.00
R / Rfree (%)	26.9 / 30.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone (pdb code 6l88). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone, PDB code: 6l88:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:0.2 occ:1.00 F1 A:E6R1001 0.0 0.2 1.0 C18 A:E6R1001 1.3 0.5 1.0 F2 A:E6R1001 2.1 1.0 1.0 F3 A:E6R1001 2.1 0.8 1.0 C17 A:E6R1001 2.4 0.7 1.0 C10 A:E6R1001 2.8 0.6 1.0 C12 A:E6R1001 2.9 0.8 1.0 N2 A:E6R1001 3.1 0.9 1.0 C11 A:E6R1001 3.3 0.7 1.0 C16 A:E6R1001 3.5 0.2 1.0 C20 A:E6R1001 3.6 0.9 1.0 C9 A:E6R1001 3.7 0.4 1.0 C8 A:E6R1001 3.8 0.7 1.0 CD1 A:LEU814 4.0 1.0 1.0 C19 A:E6R1001 4.0 0.6 1.0 CE A:MET852 4.2 0.9 1.0 C13 A:E6R1001 4.3 0.1 1.0 C15 A:E6R1001 4.7 0.7 1.0 C7 A:E6R1001 4.9 0.8 1.0 C22 A:E6R1001 5.0 0.9 1.0 CB A:SER810 5.0 0.6 1.0 C14 A:E6R1001 5.0 0.9 1.0

Fluorine binding site 2 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:1.0 occ:1.00 F2 A:E6R1001 0.0 1.0 1.0 C18 A:E6R1001 1.3 0.5 1.0 F1 A:E6R1001 2.1 0.2 1.0 F3 A:E6R1001 2.1 0.8 1.0 C17 A:E6R1001 2.4 0.7 1.0 C16 A:E6R1001 2.8 0.2 1.0 CE A:MET852 3.6 0.9 1.0 C12 A:E6R1001 3.7 0.8 1.0 C15 A:E6R1001 4.1 0.7 1.0 C10 A:E6R1001 4.2 0.6 1.0 CZ A:PHE829 4.5 0.7 1.0 C11 A:E6R1001 4.7 0.7 1.0 CE2 A:PHE829 4.7 0.4 1.0 CD1 A:LEU814 4.8 1.0 1.0 C13 A:E6R1001 4.8 0.1 1.0 N2 A:E6R1001 4.8 0.9 1.0 SG A:CYS849 4.9 0.8 1.0 C19 A:E6R1001 4.9 0.6 1.0 C14 A:E6R1001 5.0 0.9 1.0

Fluorine binding site 3 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ A:F1001 b:0.8 occ:1.00 F3 A:E6R1001 0.0 0.8 1.0 C18 A:E6R1001 1.3 0.5 1.0 F1 A:E6R1001 2.1 0.2 1.0 F2 A:E6R1001 2.1 1.0 1.0 C17 A:E6R1001 2.4 0.7 1.0 C19 A:E6R1001 2.9 0.6 1.0 C11 A:E6R1001 3.1 0.7 1.0 C12 A:E6R1001 3.1 0.8 1.0 C10 A:E6R1001 3.1 0.6 1.0 CE2 A:PHE829 3.2 0.4 1.0 CZ A:PHE829 3.3 0.7 1.0 C16 A:E6R1001 3.4 0.2 1.0 CD1 A:LEU814 3.7 1.0 1.0 C8 A:E6R1001 4.0 0.7 1.0 N2 A:E6R1001 4.1 0.9 1.0 CE A:MET852 4.2 0.9 1.0 CD2 A:PHE829 4.3 0.9 1.0 C13 A:E6R1001 4.4 0.1 1.0 CE1 A:PHE829 4.5 0.1 1.0 C9 A:E6R1001 4.6 0.4 1.0 C15 A:E6R1001 4.6 0.7 1.0 CD1 A:LEU769 4.8 99.7 1.0 C7 A:E6R1001 4.9 0.8 1.0 C14 A:E6R1001 5.0 0.9 1.0

Fluorine binding site 4 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:0.1 occ:1.00 F1 B:E6R1001 0.0 0.1 1.0 C18 B:E6R1001 1.3 0.6 1.0 F2 B:E6R1001 2.1 0.1 1.0 F3 B:E6R1001 2.1 0.5 1.0 C17 B:E6R1001 2.3 0.6 1.0 C10 B:E6R1001 2.7 0.5 1.0 C12 B:E6R1001 2.9 0.0 1.0 N2 B:E6R1001 2.9 0.5 1.0 C11 B:E6R1001 3.2 0.9 1.0 C16 B:E6R1001 3.5 0.9 1.0 C20 B:E6R1001 3.5 0.8 1.0 C9 B:E6R1001 3.6 0.3 1.0 C8 B:E6R1001 3.7 0.0 1.0 C19 B:E6R1001 3.9 0.3 1.0 CD1 B:LEU814 4.1 0.9 1.0 C13 B:E6R1001 4.2 0.9 1.0 CE B:MET852 4.3 0.6 1.0 C15 B:E6R1001 4.6 0.3 1.0 C7 B:E6R1001 4.8 0.9 1.0 C22 B:E6R1001 4.9 0.5 1.0 C14 B:E6R1001 4.9 0.5 1.0

Fluorine binding site 5 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:0.1 occ:1.00 F2 B:E6R1001 0.0 0.1 1.0 C18 B:E6R1001 1.3 0.6 1.0 F1 B:E6R1001 2.1 0.1 1.0 F3 B:E6R1001 2.1 0.5 1.0 C17 B:E6R1001 2.4 0.6 1.0 C16 B:E6R1001 2.8 0.9 1.0 C12 B:E6R1001 3.6 0.0 1.0 CE B:MET852 3.7 0.6 1.0 C15 B:E6R1001 4.1 0.3 1.0 C10 B:E6R1001 4.1 0.5 1.0 C11 B:E6R1001 4.6 0.9 1.0 C13 B:E6R1001 4.8 0.9 1.0 CD1 B:LEU814 4.8 0.9 1.0 N2 B:E6R1001 4.8 0.5 1.0 C19 B:E6R1001 4.8 0.3 1.0 C14 B:E6R1001 5.0 0.5 1.0

Fluorine binding site 6 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ B:F1001 b:0.5 occ:1.00 F3 B:E6R1001 0.0 0.5 1.0 C18 B:E6R1001 1.3 0.6 1.0 F1 B:E6R1001 2.1 0.1 1.0 F2 B:E6R1001 2.1 0.1 1.0 C17 B:E6R1001 2.4 0.6 1.0 C19 B:E6R1001 2.8 0.3 1.0 C11 B:E6R1001 3.0 0.9 1.0 C12 B:E6R1001 3.1 0.0 1.0 C10 B:E6R1001 3.1 0.5 1.0 C16 B:E6R1001 3.4 0.9 1.0 CD1 B:LEU814 3.8 0.9 1.0 C8 B:E6R1001 4.0 0.0 1.0 N2 B:E6R1001 4.1 0.5 1.0 C13 B:E6R1001 4.3 0.9 1.0 CE B:MET852 4.4 0.6 1.0 C9 B:E6R1001 4.5 0.3 1.0 C15 B:E6R1001 4.6 0.3 1.0 CD1 B:LEU769 4.7 0.8 1.0 C7 B:E6R1001 4.8 0.9 1.0 C14 B:E6R1001 5.0 0.5 1.0

Fluorine binding site 7 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:0.8 occ:1.00 F1 C:E6R1001 0.0 0.8 1.0 C18 C:E6R1001 1.3 0.4 1.0 F2 C:E6R1001 2.1 0.6 1.0 F3 C:E6R1001 2.1 0.6 1.0 C17 C:E6R1001 2.4 0.5 1.0 C10 C:E6R1001 2.7 0.1 1.0 C12 C:E6R1001 2.9 0.4 1.0 N2 C:E6R1001 3.1 0.7 1.0 C11 C:E6R1001 3.2 0.1 1.0 C16 C:E6R1001 3.5 0.8 1.0 C20 C:E6R1001 3.6 0.8 1.0 C9 C:E6R1001 3.7 0.8 1.0 C8 C:E6R1001 3.8 0.2 1.0 C19 C:E6R1001 4.0 0.4 1.0 CD1 C:LEU814 4.0 0.3 1.0 CE C:MET852 4.2 0.1 1.0 C13 C:E6R1001 4.2 0.4 1.0 C15 C:E6R1001 4.7 0.8 1.0 C7 C:E6R1001 4.9 0.4 1.0 C22 C:E6R1001 5.0 0.3 1.0 C14 C:E6R1001 5.0 0.1 1.0 CB C:SER810 5.0 0.3 1.0 SD C:MET807 5.0 0.5 1.0

Fluorine binding site 8 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:0.6 occ:1.00 F2 C:E6R1001 0.0 0.6 1.0 C18 C:E6R1001 1.3 0.4 1.0 F1 C:E6R1001 2.1 0.8 1.0 F3 C:E6R1001 2.1 0.6 1.0 C17 C:E6R1001 2.4 0.5 1.0 C16 C:E6R1001 2.8 0.8 1.0 C12 C:E6R1001 3.6 0.4 1.0 CE C:MET852 3.7 0.1 1.0 C15 C:E6R1001 4.1 0.8 1.0 C10 C:E6R1001 4.2 0.1 1.0 C11 C:E6R1001 4.7 0.1 1.0 C13 C:E6R1001 4.8 0.4 1.0 CD1 C:LEU814 4.8 0.3 1.0 N2 C:E6R1001 4.9 0.7 1.0 C19 C:E6R1001 4.9 0.4 1.0 C14 C:E6R1001 5.0 0.1 1.0

Fluorine binding site 9 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


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 Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ C:F1001 b:0.6 occ:1.00 F3 C:E6R1001 0.0 0.6 1.0 C18 C:E6R1001 1.3 0.4 1.0 F1 C:E6R1001 2.1 0.8 1.0 F2 C:E6R1001 2.1 0.6 1.0 C17 C:E6R1001 2.4 0.5 1.0 C19 C:E6R1001 2.9 0.4 1.0 C11 C:E6R1001 3.1 0.1 1.0 C12 C:E6R1001 3.1 0.4 1.0 C10 C:E6R1001 3.2 0.1 1.0 C16 C:E6R1001 3.4 0.8 1.0 CD1 C:LEU814 3.7 0.3 1.0 C8 C:E6R1001 4.1 0.2 1.0 N2 C:E6R1001 4.2 0.7 1.0 CE C:MET852 4.2 0.1 1.0 C13 C:E6R1001 4.4 0.4 1.0 C15 C:E6R1001 4.6 0.8 1.0 C9 C:E6R1001 4.6 0.8 1.0 CD1 C:LEU769 4.8 0.8 1.0 C7 C:E6R1001 4.9 0.4 1.0

Fluorine binding site 10 out of 12 in the Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Mineralocorticoid Receptor Ligand Binding Domain in Complex with Esaxerenone within 5.0Å range: probe atom residue distance (Å) B Occ D:F1001 b:0.2 occ:1.00 F1 D:E6R1001 0.0 0.2 1.0 C18 D:E6R1001 1.3 0.9 1.0 F2 D:E6R1001 2.1 0.7 1.0 F3 D:E6R1001 2.1 0.6 1.0 C17 D:E6R1001 2.3 0.1 1.0 C10 D:E6R1001 2.8 0.0 1.0 C12 D:E6R1001 2.9 0.0 1.0 N2 D:E6R1001 3.0 0.5 1.0 C11 D:E6R1001 3.3 0.5 1.0 C16 D:E6R1001 3.5 0.7 1.0 C20 D:E6R1001 3.6 0.1 1.0 C9 D:E6R1001 3.7 0.1 1.0 C8 D:E6R1001 3.8 0.4 1.0 C19 D:E6R1001 4.0 0.2 1.0 CD1 D:LEU814 4.1 0.3 1.0 C13 D:E6R1001 4.2 0.3 1.0 CE D:MET852 4.2 0.0 1.0 C15 D:E6R1001 4.7 0.7 1.0 C7 D:E6R1001 4.9 0.3 1.0 C14 D:E6R1001 4.9 0.2 1.0 C22 D:E6R1001 5.0 0.1 1.0

M.Takahashi, O.Ubukata, T.Homma, Y.Asoh, M.Honzumi, N.Hayashi, K.Saito, H.Tsuruoka, K.Aoki, H.Hanzawa. Crystal Structure of the Mineralocorticoid Receptor Ligand-Binding Domain in Complex with A Potent and Selective Nonsteroidal Blocker, Esaxerenone (Cs-3150). Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 31991486
DOI: 10.1002/1873-3468.13746