Fluorine in PDB 5g5w: Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators

The structure of Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators, PDB code: 5g5w was solved by M.Hemmerling, K.Edman, M.Lepisto, A.Eriksson, S.Ivanova, J.Dahmen, H.Rehwinkel, M.Berger, R.Hendrickx, M.Dearman, T.Jellesmark-Jensen, L.Wissler, T.Hansson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.74 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.880, 83.880, 105.700, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21

The binding sites of Fluorine atom in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators (pdb code 5g5w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators, PDB code: 5g5w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators within 5.0Å range: probe atom residue distance (Å) B Occ A:F1778 b:35.0 occ:1.00 F28 A:R8C1778 0.0 35.0 1.0 C25 A:R8C1778 1.3 28.8 1.0 C24 A:R8C1778 2.4 22.9 1.0 C26 A:R8C1778 2.4 28.7 1.0 O A:ALA607 3.2 31.2 1.0 C A:ALA607 3.2 30.9 1.0 NH2 A:ARG611 3.3 28.1 1.0 CZ A:ARG611 3.4 47.8 1.0 N A:LEU608 3.4 28.6 1.0 NE A:ARG611 3.6 41.5 1.0 CA A:LEU608 3.6 28.6 1.0 C23 A:R8C1778 3.6 23.9 1.0 C27 A:R8C1778 3.6 26.4 1.0 CB A:ALA607 3.7 25.5 1.0 CB A:ARG611 3.9 35.0 1.0 O A:HOH2055 3.9 41.1 1.0 NH1 A:ARG611 3.9 28.4 1.0 CA A:ALA607 4.0 25.9 1.0 C22 A:R8C1778 4.1 28.2 1.0 O A:HOH2129 4.2 34.7 1.0 O A:HOH2059 4.3 62.6 1.0 CG A:ARG611 4.3 41.2 1.0 CB A:LEU608 4.4 27.9 1.0 CD A:ARG611 4.5 42.0 1.0 O A:HOH2130 4.6 42.5 1.0 C A:LEU608 4.8 33.2 1.0 O A:HOH2057 4.9 43.0 1.0 O A:MET604 5.0 27.7 1.0

Fluorine binding site 2 out of 4 in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators within 5.0Å range: probe atom residue distance (Å) B Occ A:F1778 b:33.4 occ:1.00 F33 A:R8C1778 0.0 33.4 1.0 C32 A:R8C1778 1.4 32.6 1.0 F35 A:R8C1778 2.2 33.3 1.0 F34 A:R8C1778 2.3 34.2 1.0 C30 A:R8C1778 2.4 31.1 1.0 O31 A:R8C1778 2.8 29.2 1.0 CB A:THR739 3.4 36.6 1.0 N29 A:R8C1778 3.4 28.2 1.0 CA A:CYS736 3.5 31.6 1.0 CD1 A:TYR735 3.5 47.5 1.0 OG1 A:THR739 3.5 38.0 1.0 CG2 A:THR739 3.6 34.6 1.0 CE1 A:TYR735 3.6 50.7 1.0 O A:TYR735 4.0 40.6 1.0 CZ A:PHE749 4.0 26.8 1.0 CB A:CYS736 4.1 30.9 1.0 N A:CYS736 4.1 33.9 1.0 O A:CYS736 4.2 33.3 1.0 C A:TYR735 4.3 40.4 1.0 SG A:CYS736 4.4 33.5 1.0 C A:CYS736 4.4 34.4 1.0 NE2 A:GLN642 4.5 36.0 1.0 CE2 A:PHE749 4.6 28.8 1.0 SD A:MET560 4.7 57.5 1.0 C2 A:R8C1778 4.7 30.0 1.0 CG A:TYR735 4.8 46.7 1.0 CA A:THR739 4.8 33.5 1.0 CZ A:TYR735 4.9 64.6 1.0 OD1 A:ASN564 5.0 23.8 1.0 CE1 A:PHE749 5.0 28.1 1.0

Fluorine binding site 3 out of 4 in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators within 5.0Å range: probe atom residue distance (Å) B Occ A:F1778 b:34.2 occ:1.00 F34 A:R8C1778 0.0 34.2 1.0 C32 A:R8C1778 1.4 32.6 1.0 F35 A:R8C1778 2.2 33.3 1.0 F33 A:R8C1778 2.3 33.4 1.0 C30 A:R8C1778 2.3 31.1 1.0 O31 A:R8C1778 2.9 29.2 1.0 SD A:MET560 3.2 57.5 1.0 CE1 A:TYR735 3.3 50.7 1.0 N29 A:R8C1778 3.3 28.2 1.0 CD1 A:TYR735 3.7 47.5 1.0 CG A:MET560 4.0 48.6 1.0 C11 A:R8C1778 4.0 28.5 1.0 C10 A:R8C1778 4.1 29.1 1.0 CG A:GLN642 4.3 43.1 1.0 NE2 A:GLN642 4.3 36.0 1.0 C6 A:R8C1778 4.4 26.3 1.0 CZ A:TYR735 4.5 64.6 1.0 CB A:MET560 4.5 39.9 1.0 C9 A:R8C1778 4.6 25.0 1.0 C2 A:R8C1778 4.6 30.0 1.0 CE A:MET560 4.7 56.2 1.0 OH A:TYR735 4.7 71.8 1.0 CD A:GLN642 4.8 48.1 1.0 OD1 A:ASN564 4.8 23.8 1.0 C7 A:R8C1778 4.9 26.4 1.0 CG2 A:THR739 4.9 34.6 1.0 C8 A:R8C1778 4.9 25.0 1.0 OG1 A:THR739 5.0 38.0 1.0 CB A:GLN642 5.0 45.0 1.0

Fluorine binding site 4 out of 4 in the Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure Guided Design and Discovery of Indazole Ethers As Highly Potent, Non-Steroidal Glucocorticoid Receptor Modulators within 5.0Å range: probe atom residue distance (Å) B Occ A:F1778 b:33.3 occ:1.00 F35 A:R8C1778 0.0 33.3 1.0 C32 A:R8C1778 1.4 32.6 1.0 F33 A:R8C1778 2.2 33.4 1.0 F34 A:R8C1778 2.2 34.2 1.0 C30 A:R8C1778 2.4 31.1 1.0 N29 A:R8C1778 2.7 28.2 1.0 OD1 A:ASN564 3.1 23.8 1.0 ND2 A:ASN564 3.2 24.8 1.0 CG A:ASN564 3.5 30.4 1.0 O31 A:R8C1778 3.6 29.2 1.0 CZ A:PHE749 3.7 26.8 1.0 CG2 A:ILE747 4.0 32.4 1.0 CG2 A:THR739 4.1 34.6 1.0 SD A:MET560 4.1 57.5 1.0 CE2 A:PHE749 4.1 28.8 1.0 C2 A:R8C1778 4.2 30.0 1.0 CB A:MET560 4.3 39.9 1.0 O A:MET560 4.4 30.9 1.0 C11 A:R8C1778 4.5 28.5 1.0 CE1 A:PHE749 4.6 28.1 1.0 CG A:MET560 4.6 48.6 1.0 CB A:THR739 4.7 36.6 1.0 C1 A:R8C1778 4.9 29.5 1.0 C6 A:R8C1778 4.9 26.3 1.0 C4 A:R8C1778 4.9 29.2 1.0 CE1 A:TYR735 5.0 50.7 1.0 C A:MET560 5.0 34.2 1.0

M.Hemmerling, K.Edman, M.Lepisto, A.Eriksson, S.Ivanova, J.Dahmen, H.Rehwinkel, M.Berger, R.Hendrickx, M.Dearman, T.J.Jensen, L.Wissler, T.Hansson. Discovery of Indazole Ethers As Novel, Potent, Non-Steroidal Glucocorticoid Receptor Modulators. Bioorg.Med.Chem.Lett. V. 26 5741 2017.
ISSN: ISSN 0960-894X
PubMed: 27810243
DOI: 10.1016/J.BMCL.2016.10.052