Fluorine in PDB 3k23: Glucocorticoid Receptor with Bound D-Prolinamide 11

The structure of Glucocorticoid Receptor with Bound D-Prolinamide 11, PDB code: 3k23 was solved by K.B.Biggadike, I.M.Mclay, K.P.Madauss, S.P.Williams, R.K.Bledsoe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.82 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.927, 65.956, 71.528, 90.00, 103.64, 90.00
R / Rfree (%)	22.4 / 28.9

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Glucocorticoid Receptor with Bound D-Prolinamide 11 (pdb code 3k23). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Glucocorticoid Receptor with Bound D-Prolinamide 11, PDB code: 3k23:
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 Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:58.9 occ:1.00 F1 A:JZN1 0.0 58.9 1.0 C5 A:JZN1 1.3 59.0 1.0 C4 A:JZN1 2.3 59.3 1.0 C6 A:JZN1 2.4 59.1 1.0 CD1 A:LEU563 3.4 54.9 1.0 C3 A:JZN1 3.6 59.2 1.0 C7 A:JZN1 3.6 59.1 1.0 CE A:MET560 4.0 60.2 1.0 C2 A:JZN1 4.1 58.9 1.0 CB A:MET639 4.2 74.0 1.0 CZ A:PHE623 4.6 43.8 1.0 C8 A:JZN1 4.8 59.2 1.0 CG A:LEU563 4.8 55.5 1.0 C13 A:JZN1 5.0 59.3 1.0

Fluorine binding site 2 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:59.5 occ:1.00 F2 A:JZN1 0.0 59.5 1.0 C34 A:JZN1 1.4 59.5 1.0 F4 A:JZN1 2.2 60.6 1.0 F3 A:JZN1 2.2 60.6 1.0 O2 A:JZN1 2.2 60.0 1.0 C12 A:JZN1 2.4 59.1 1.0 CD1 A:LEU753 2.9 64.3 1.0 C11 A:JZN1 3.3 59.0 1.0 C13 A:JZN1 3.5 59.3 1.0 CA A:ASN564 3.6 53.9 1.0 N1 A:JZN1 3.6 59.0 1.0 O A:LEU563 3.6 54.4 1.0 OD1 A:ASN564 3.8 53.6 1.0 O A:ASN564 4.0 53.7 1.0 N A:ASN564 4.1 54.2 1.0 CA A:GLY567 4.1 49.7 1.0 C A:LEU563 4.1 54.7 1.0 C A:ASN564 4.3 53.7 1.0 CG A:LEU753 4.4 65.5 1.0 C9 A:JZN1 4.4 60.0 1.0 C8 A:JZN1 4.5 59.2 1.0 CB A:ASN564 4.5 53.9 1.0 CG A:ASN564 4.6 53.8 1.0 C14 A:JZN1 4.6 58.7 1.0 N A:GLY567 4.6 50.0 1.0 CE2 A:PHE749 4.8 70.2 1.0 C A:GLY567 4.9 49.4 1.0 CD2 A:LEU753 4.9 65.1 1.0

Fluorine binding site 3 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:60.6 occ:1.00 F3 A:JZN1 0.0 60.6 1.0 C34 A:JZN1 1.4 59.5 1.0 F2 A:JZN1 2.2 59.5 1.0 F4 A:JZN1 2.2 60.6 1.0 C12 A:JZN1 2.4 59.1 1.0 C13 A:JZN1 2.6 59.3 1.0 N1 A:JZN1 2.9 59.0 1.0 O2 A:JZN1 3.1 60.0 1.0 C14 A:JZN1 3.4 58.7 1.0 C15 A:JZN1 3.6 58.6 1.0 C1 A:JZN1 3.7 59.2 1.0 C11 A:JZN1 3.7 59.0 1.0 CE A:MET601 4.1 47.3 1.0 C9 A:JZN1 4.2 60.0 1.0 CZ3 A:TRP600 4.3 46.9 1.0 SD A:MET604 4.3 45.2 1.0 C8 A:JZN1 4.3 59.2 1.0 CD1 A:LEU753 4.4 64.3 1.0 C21 A:JZN1 4.4 59.1 1.0 O1 A:JZN1 4.6 59.0 1.0 C16 A:JZN1 4.7 58.9 1.0 C7 A:JZN1 4.8 59.1 1.0 CA A:GLY567 4.8 49.7 1.0 SD A:MET601 4.8 47.0 1.0 CH2 A:TRP600 4.8 47.0 1.0 O A:LEU563 4.9 54.4 1.0 C2 A:JZN1 4.9 58.9 1.0 SG A:CYS736 4.9 57.9 1.0

Fluorine binding site 4 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:60.6 occ:1.00 F4 A:JZN1 0.0 60.6 1.0 C34 A:JZN1 1.3 59.5 1.0 F2 A:JZN1 2.2 59.5 1.0 F3 A:JZN1 2.2 60.6 1.0 C12 A:JZN1 2.4 59.1 1.0 C9 A:JZN1 2.5 60.0 1.0 C11 A:JZN1 2.8 59.0 1.0 C8 A:JZN1 3.2 59.2 1.0 O2 A:JZN1 3.3 60.0 1.0 SG A:CYS736 3.4 57.9 1.0 C13 A:JZN1 3.4 59.3 1.0 C1 A:JZN1 3.8 59.2 1.0 OD1 A:ASN564 4.0 53.6 1.0 O1 A:JZN1 4.1 59.0 1.0 C7 A:JZN1 4.2 59.1 1.0 CD1 A:LEU753 4.2 64.3 1.0 CB A:CYS736 4.2 58.0 1.0 N1 A:JZN1 4.3 59.0 1.0 C10 A:JZN1 4.3 58.6 1.0 CE2 A:PHE749 4.5 70.2 1.0 C2 A:JZN1 4.5 58.9 1.0 CE A:MET601 4.7 47.3 1.0 CZ A:PHE749 4.7 70.3 1.0 CH2 A:TRP600 4.9 47.0 1.0 CA A:CYS736 4.9 58.1 1.0 CZ3 A:TRP600 4.9 46.9 1.0

Fluorine binding site 5 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:54.6 occ:1.00 F1 B:JZN2 0.0 54.6 1.0 C5 B:JZN2 1.4 55.1 1.0 C6 B:JZN2 2.3 54.5 1.0 C4 B:JZN2 2.4 55.1 1.0 O B:LEU732 2.9 41.5 1.0 OE1 B:GLN642 3.2 50.4 1.0 C B:LEU732 3.6 41.4 1.0 CA B:LEU732 3.6 41.3 1.0 CB B:LEU732 3.6 41.0 1.0 C3 B:JZN2 3.6 54.4 1.0 C7 B:JZN2 3.6 54.4 1.0 CD2 B:TYR735 4.0 44.4 1.0 CE B:MET601 4.0 42.2 1.0 CD2 B:LEU732 4.0 37.5 1.0 C2 B:JZN2 4.1 54.4 1.0 CB B:CYS736 4.1 45.1 1.0 CD B:GLN642 4.3 50.1 1.0 N B:CYS736 4.3 44.9 1.0 CB B:TYR735 4.3 43.5 1.0 CG B:LEU732 4.4 39.8 1.0 CG B:TYR735 4.6 43.8 1.0 CA B:CYS736 4.6 45.3 1.0 CE B:MET646 4.7 48.1 1.0 F4 B:JZN2 4.8 49.5 1.0 C8 B:JZN2 4.8 54.7 1.0 SD B:MET601 4.8 46.8 1.0 C13 B:JZN2 4.8 55.1 1.0 N B:LEU733 4.8 41.7 1.0 C11 B:JZN2 4.9 54.3 1.0 CE2 B:TYR735 4.9 43.6 1.0 CD1 B:LEU732 5.0 37.7 1.0 N B:LEU732 5.0 41.6 1.0

Fluorine binding site 6 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:55.4 occ:1.00 F2 B:JZN2 0.0 55.4 1.0 C34 B:JZN2 1.2 52.3 1.0 F3 B:JZN2 2.2 51.6 1.0 F4 B:JZN2 2.2 49.5 1.0 C12 B:JZN2 2.3 53.8 1.0 O2 B:JZN2 2.6 52.8 1.0 C11 B:JZN2 2.7 54.3 1.0 OD1 B:ASN564 2.9 50.5 1.0 CD1 B:LEU753 3.5 49.3 1.0 C13 B:JZN2 3.6 55.1 1.0 CG B:ASN564 3.8 50.2 1.0 N1 B:JZN2 4.0 55.9 1.0 CD2 B:LEU753 4.1 50.4 1.0 CA B:ASN564 4.2 49.8 1.0 C8 B:JZN2 4.2 54.7 1.0 CG B:LEU753 4.3 50.7 1.0 SG B:CYS736 4.4 45.0 1.0 CB B:ASN564 4.5 49.6 1.0 CE2 B:PHE749 4.5 57.5 1.0 ND2 B:ASN564 4.6 49.8 1.0 CZ3 B:TRP600 4.7 46.7 1.0 C10 B:JZN2 4.7 54.8 1.0 CH2 B:TRP600 4.7 46.5 1.0 O B:LEU563 4.8 49.7 1.0 N B:ASN564 4.8 49.6 1.0 CD2 B:PHE749 4.8 57.6 1.0 CB B:LEU753 4.9 51.6 1.0 C9 B:JZN2 5.0 54.3 1.0

Fluorine binding site 7 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:51.6 occ:1.00 F3 B:JZN2 0.0 51.6 1.0 C34 B:JZN2 1.5 52.3 1.0 F2 B:JZN2 2.2 55.4 1.0 F4 B:JZN2 2.2 49.5 1.0 C12 B:JZN2 2.3 53.8 1.0 N1 B:JZN2 2.5 55.9 1.0 O2 B:JZN2 2.7 52.8 1.0 C13 B:JZN2 2.8 55.1 1.0 C14 B:JZN2 3.3 55.8 1.0 C11 B:JZN2 3.7 54.3 1.0 O B:LEU563 3.9 49.7 1.0 C21 B:JZN2 3.9 56.0 1.0 CA B:GLY567 4.0 49.5 1.0 C15 B:JZN2 4.1 56.1 1.0 SD B:MET604 4.2 44.1 1.0 C20 B:JZN2 4.2 55.8 1.0 CD1 B:LEU753 4.2 49.3 1.0 OD1 B:ASN564 4.3 50.5 1.0 CD2 B:LEU753 4.5 50.4 1.0 CZ3 B:TRP600 4.5 46.7 1.0 C B:LEU563 4.5 49.4 1.0 CA B:ASN564 4.6 49.8 1.0 N B:GLY567 4.7 49.4 1.0 C B:GLY567 4.8 49.6 1.0 N B:ASN564 4.9 49.6 1.0 C8 B:JZN2 5.0 54.7 1.0

Fluorine binding site 8 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:49.5 occ:1.00 F4 B:JZN2 0.0 49.5 1.0 C34 B:JZN2 1.3 52.3 1.0 F2 B:JZN2 2.2 55.4 1.0 F3 B:JZN2 2.2 51.6 1.0 C12 B:JZN2 2.4 53.8 1.0 C11 B:JZN2 2.9 54.3 1.0 C13 B:JZN2 2.9 55.1 1.0 N1 B:JZN2 3.5 55.9 1.0 CE B:MET601 3.5 42.2 1.0 O2 B:JZN2 3.6 52.8 1.0 SG B:CYS736 3.8 45.0 1.0 C6 B:JZN2 3.9 54.5 1.0 CZ3 B:TRP600 3.9 46.7 1.0 CH2 B:TRP600 4.0 46.5 1.0 C14 B:JZN2 4.2 55.8 1.0 C8 B:JZN2 4.3 54.7 1.0 C15 B:JZN2 4.3 56.1 1.0 C7 B:JZN2 4.5 54.4 1.0 CB B:CYS736 4.5 45.1 1.0 OD1 B:ASN564 4.7 50.5 1.0 C5 B:JZN2 4.7 55.1 1.0 SD B:MET601 4.7 46.8 1.0 F1 B:JZN2 4.8 54.6 1.0 CD2 B:LEU753 5.0 50.4 1.0

Fluorine binding site 9 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ C:F3 b:77.9 occ:1.00 F1 C:JZN3 0.0 77.9 1.0 C5 C:JZN3 1.3 77.4 1.0 C6 C:JZN3 2.3 77.0 1.0 C4 C:JZN3 2.4 77.2 1.0 CD2 C:LEU732 3.4 87.9 1.0 CB C:LEU732 3.5 88.3 1.0 C7 C:JZN3 3.6 77.0 1.0 C3 C:JZN3 3.6 76.7 1.0 CG C:LEU732 3.6 88.1 1.0 CD1 C:LEU732 3.7 88.1 1.0 CA C:LEU732 4.0 88.3 1.0 C2 C:JZN3 4.1 77.1 1.0 CE C:MET646 4.3 81.8 1.0 CB C:CYS736 4.6 93.0 1.0 CD2 C:TYR735 4.7 92.5 1.0 C C:LEU732 4.7 88.6 1.0 O C:LEU732 4.7 88.7 1.0 C8 C:JZN3 4.8 77.2 1.0 C9 C:JZN3 4.8 76.8 1.0 F4 C:JZN3 4.8 77.1 1.0 C13 C:JZN3 4.9 77.7 1.0 N C:CYS736 5.0 92.7 1.0 CE C:MET601 5.0 71.1 1.0

Fluorine binding site 10 out of 12 in the Glucocorticoid Receptor with Bound D-Prolinamide 11


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Glucocorticoid Receptor with Bound D-Prolinamide 11 within 5.0Å range: probe atom residue distance (Å) B Occ C:F3 b:77.9 occ:1.00 F2 C:JZN3 0.0 77.9 1.0 C34 C:JZN3 1.4 77.6 1.0 F3 C:JZN3 2.2 78.6 1.0 F4 C:JZN3 2.2 77.1 1.0 C12 C:JZN3 2.4 77.5 1.0 C9 C:JZN3 2.8 76.8 1.0 C11 C:JZN3 2.9 77.4 1.0 O2 C:JZN3 2.9 78.1 1.0 OD1 C:ASN564 3.3 65.7 1.0 C8 C:JZN3 3.3 77.2 1.0 CD1 C:LEU753 3.6 88.5 1.0 C13 C:JZN3 3.7 77.7 1.0 CG C:ASN564 3.8 65.2 1.0 CA C:ASN564 4.0 64.4 1.0 SG C:CYS736 4.0 92.7 1.0 CE2 C:PHE749 4.2 88.0 1.0 N1 C:JZN3 4.2 78.6 1.0 C10 C:JZN3 4.3 76.4 1.0 CB C:ASN564 4.4 64.7 1.0 C7 C:JZN3 4.5 77.0 1.0 ND2 C:ASN564 4.5 66.1 1.0 CZ C:PHE749 4.5 88.3 1.0 C6 C:JZN3 4.6 77.0 1.0 N C:ASN564 4.6 64.2 1.0 O C:LEU563 4.8 64.3 1.0 CD2 C:PHE749 4.9 88.3 1.0 CG C:LEU753 4.9 89.1 1.0 O C:ASN564 5.0 64.4 1.0 C C:LEU563 5.0 64.3 1.0

K.Biggadike, R.K.Bledsoe, D.M.Coe, T.W.Cooper, D.House, M.A.Iannone, S.J.Macdonald, K.P.Madauss, I.M.Mclay, T.J.Shipley, S.J.Taylor, T.B.Tran, I.J.Uings, V.Weller, S.P.Williams. Design and X-Ray Crystal Structures of High-Potency Nonsteroidal Glucocorticoid Agonists Exploiting A Novel Binding Site on the Receptor. Proc.Natl.Acad.Sci.Usa V. 106 18114 2009.
ISSN: ISSN 0027-8424
PubMed: 19822747
DOI: 10.1073/PNAS.0909125106