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Fluorine in PDB 5v8q: Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III

Protein crystallography data

The structure of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III, PDB code: 5v8q was solved by K.P.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.15 / 1.44
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.747, 65.557, 70.941, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III (pdb code 5v8q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III, PDB code: 5v8q:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 1 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:18.3
occ:0.50
F21 A:97A1004 0.0 18.3 0.5
F21 A:97A1004 0.4 17.4 0.5
C20 A:97A1004 1.4 18.3 0.5
C20 A:97A1004 1.4 18.4 0.5
F23 A:97A1004 2.1 19.6 0.5
F23 A:97A1004 2.3 18.3 0.5
F22 A:97A1004 2.3 17.9 0.5
C18 A:97A1004 2.4 17.5 0.5
C18 A:97A1004 2.4 17.2 0.5
F22 A:97A1004 2.4 18.8 0.5
C19 A:97A1004 2.7 17.9 0.5
C19 A:97A1004 2.7 18.1 0.5
SD A:MET787 3.3 23.4 1.0
CE1 A:PHE764 3.5 16.7 1.0
CD1 A:LEU873 3.6 20.7 1.0
C15 A:97A1004 3.6 17.9 0.5
C15 A:97A1004 3.7 17.8 0.5
CG2 A:VAL746 3.8 15.5 0.3
O10 A:97A1004 4.0 19.4 0.5
O10 A:97A1004 4.0 20.1 0.5
CG2 A:VAL746 4.1 18.4 0.7
C12 A:97A1004 4.1 18.1 0.5
CE A:MET749 4.1 18.8 1.0
C12 A:97A1004 4.1 18.3 0.5
CE A:MET787 4.1 22.8 1.0
C16 A:97A1004 4.2 18.0 0.5
CD1 A:PHE764 4.3 15.2 1.0
C16 A:97A1004 4.3 20.0 0.5
CB A:VAL746 4.3 17.7 0.7
CA A:VAL746 4.5 15.2 1.0
CZ A:PHE764 4.5 16.6 1.0
CD2 A:LEU873 4.7 20.8 1.0
CB A:VAL746 4.7 15.8 0.3
C14 A:97A1004 4.7 17.8 0.5
CG A:LEU873 4.8 19.2 1.0
C14 A:97A1004 4.8 16.2 0.5
C9 A:97A1004 4.8 18.8 0.5
C9 A:97A1004 4.9 19.3 0.5
N A:VAL746 4.9 14.2 1.0
N11 A:97A1004 4.9 19.2 0.5
C13 A:97A1004 4.9 18.9 0.5
N11 A:97A1004 4.9 19.1 0.5
C13 A:97A1004 4.9 17.6 0.5
N17 A:97A1004 5.0 19.7 0.5
CG A:MET787 5.0 20.1 1.0

Fluorine binding site 2 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 2 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:17.4
occ:0.50
F21 A:97A1004 0.0 17.4 0.5
F21 A:97A1004 0.4 18.3 0.5
C20 A:97A1004 1.3 18.3 0.5
C20 A:97A1004 1.4 18.4 0.5
F22 A:97A1004 2.0 17.9 0.5
F22 A:97A1004 2.2 18.8 0.5
F23 A:97A1004 2.3 19.6 0.5
C18 A:97A1004 2.3 17.5 0.5
F23 A:97A1004 2.3 18.3 0.5
C18 A:97A1004 2.4 17.2 0.5
C19 A:97A1004 2.6 17.9 0.5
C19 A:97A1004 2.6 18.1 0.5
CD1 A:LEU873 3.4 20.7 1.0
SD A:MET787 3.4 23.4 1.0
CG2 A:VAL746 3.5 15.5 0.3
C15 A:97A1004 3.6 17.9 0.5
C15 A:97A1004 3.7 17.8 0.5
CE1 A:PHE764 3.9 16.7 1.0
CG2 A:VAL746 4.0 18.4 0.7
O10 A:97A1004 4.0 19.4 0.5
C12 A:97A1004 4.0 18.1 0.5
C12 A:97A1004 4.0 18.3 0.5
O10 A:97A1004 4.1 20.1 0.5
CB A:VAL746 4.2 17.7 0.7
C16 A:97A1004 4.2 18.0 0.5
C16 A:97A1004 4.3 20.0 0.5
CE A:MET787 4.3 22.8 1.0
CA A:VAL746 4.3 15.2 1.0
CE A:MET749 4.3 18.8 1.0
CB A:VAL746 4.5 15.8 0.3
CD1 A:PHE764 4.6 15.2 1.0
CD2 A:LEU873 4.6 20.8 1.0
CG A:LEU873 4.6 19.2 1.0
N A:VAL746 4.7 14.2 1.0
C14 A:97A1004 4.7 17.8 0.5
C14 A:97A1004 4.8 16.2 0.5
C9 A:97A1004 4.8 19.3 0.5
C9 A:97A1004 4.8 18.8 0.5
N11 A:97A1004 4.8 19.2 0.5
CZ A:PHE764 4.8 16.6 1.0
SD A:MET742 4.9 19.8 1.0
N11 A:97A1004 4.9 19.1 0.5
C13 A:97A1004 4.9 18.9 0.5
C13 A:97A1004 4.9 17.6 0.5
N17 A:97A1004 5.0 19.7 0.5

Fluorine binding site 3 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 3 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:17.9
occ:0.50
F22 A:97A1004 0.0 17.9 0.5
F22 A:97A1004 0.6 18.8 0.5
C20 A:97A1004 1.4 18.3 0.5
C20 A:97A1004 1.5 18.4 0.5
F21 A:97A1004 2.0 17.4 0.5
F21 A:97A1004 2.3 18.3 0.5
F23 A:97A1004 2.3 18.3 0.5
C18 A:97A1004 2.4 17.5 0.5
C18 A:97A1004 2.4 17.2 0.5
F23 A:97A1004 2.6 19.6 0.5
C19 A:97A1004 3.1 17.9 0.5
C19 A:97A1004 3.1 18.1 0.5
CG2 A:VAL746 3.2 15.5 0.3
N A:VAL746 3.2 14.2 1.0
CB A:MET745 3.3 16.4 1.0
C15 A:97A1004 3.3 17.8 0.5
C15 A:97A1004 3.3 17.9 0.5
CA A:VAL746 3.5 15.2 1.0
C A:MET745 3.5 14.5 1.0
C16 A:97A1004 3.6 20.0 0.5
C16 A:97A1004 3.6 18.0 0.5
CB A:VAL746 3.7 17.7 0.7
O A:MET742 3.9 15.2 1.0
O A:MET745 3.9 16.3 1.0
CB A:VAL746 3.9 15.8 0.3
CE A:MET745 4.0 17.8 1.0
CA A:MET745 4.0 15.1 1.0
CD1 A:LEU873 4.2 20.7 1.0
SD A:MET742 4.2 19.8 1.0
N17 A:97A1004 4.2 23.4 0.5
CG2 A:VAL746 4.2 18.4 0.7
N17 A:97A1004 4.2 19.7 0.5
C12 A:97A1004 4.4 18.1 0.5
C12 A:97A1004 4.4 18.3 0.5
C14 A:97A1004 4.5 16.2 0.5
CG A:MET745 4.5 17.1 1.0
C14 A:97A1004 4.5 17.8 0.5
SD A:MET745 4.6 17.3 1.0
C A:VAL746 4.9 14.9 1.0
C13 A:97A1004 4.9 17.6 0.5
C A:MET742 4.9 15.4 1.0
N A:MET745 4.9 14.3 1.0
C13 A:97A1004 4.9 18.9 0.5
CG1 A:VAL746 5.0 17.6 0.7
CG A:MET742 5.0 17.5 1.0

Fluorine binding site 4 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 4 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:18.8
occ:0.50
F22 A:97A1004 0.0 18.8 0.5
F22 A:97A1004 0.6 17.9 0.5
C20 A:97A1004 1.4 18.3 0.5
C20 A:97A1004 1.4 18.4 0.5
F23 A:97A1004 1.8 18.3 0.5
F21 A:97A1004 2.2 17.4 0.5
F23 A:97A1004 2.3 19.6 0.5
C18 A:97A1004 2.4 17.2 0.5
C18 A:97A1004 2.4 17.5 0.5
F21 A:97A1004 2.4 18.3 0.5
CB A:MET745 3.0 16.4 1.0
N A:VAL746 3.0 14.2 1.0
C15 A:97A1004 3.1 17.8 0.5
C15 A:97A1004 3.1 17.9 0.5
C A:MET745 3.1 14.5 1.0
C16 A:97A1004 3.2 20.0 0.5
C16 A:97A1004 3.2 18.0 0.5
CA A:VAL746 3.3 15.2 1.0
C19 A:97A1004 3.4 17.9 0.5
C19 A:97A1004 3.4 18.1 0.5
O A:MET745 3.4 16.3 1.0
CG2 A:VAL746 3.5 15.5 0.3
N17 A:97A1004 3.7 23.4 0.5
N17 A:97A1004 3.7 19.7 0.5
CA A:MET745 3.7 15.1 1.0
CB A:VAL746 3.8 17.7 0.7
CB A:VAL746 4.0 15.8 0.3
CE A:MET745 4.1 17.8 1.0
O A:MET742 4.1 15.2 1.0
CG A:MET745 4.3 17.1 1.0
CG2 A:VAL746 4.3 18.4 0.7
C14 A:97A1004 4.4 16.2 0.5
C14 A:97A1004 4.4 17.8 0.5
SD A:MET745 4.4 17.3 1.0
C12 A:97A1004 4.6 18.1 0.5
CB A:MET749 4.6 15.4 1.0
C12 A:97A1004 4.6 18.3 0.5
C A:VAL746 4.7 14.9 1.0
CD1 A:LEU873 4.7 20.7 1.0
SD A:MET742 4.7 19.8 1.0
N A:MET745 4.8 14.3 1.0
C13 A:97A1004 5.0 17.6 0.5

Fluorine binding site 5 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 5 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:18.3
occ:0.50
F23 A:97A1004 0.0 18.3 0.5
F23 A:97A1004 0.5 19.6 0.5
C20 A:97A1004 1.3 18.4 0.5
C20 A:97A1004 1.4 18.3 0.5
F22 A:97A1004 1.8 18.8 0.5
F21 A:97A1004 2.3 18.3 0.5
F22 A:97A1004 2.3 17.9 0.5
F21 A:97A1004 2.3 17.4 0.5
C18 A:97A1004 2.4 17.2 0.5
C18 A:97A1004 2.4 17.5 0.5
C16 A:97A1004 2.6 18.0 0.5
C16 A:97A1004 2.7 20.0 0.5
C15 A:97A1004 2.9 17.9 0.5
C15 A:97A1004 2.9 17.8 0.5
N17 A:97A1004 3.0 19.7 0.5
N17 A:97A1004 3.1 23.4 0.5
CB A:MET749 3.3 15.4 1.0
C19 A:97A1004 3.6 17.9 0.5
CG A:MET749 3.6 16.5 1.0
C19 A:97A1004 3.6 18.1 0.5
CD1 A:PHE764 3.7 15.2 1.0
O A:MET745 3.7 16.3 1.0
CE1 A:PHE764 3.7 16.7 1.0
CE A:MET749 3.8 18.8 1.0
C A:MET745 4.0 14.5 1.0
CA A:VAL746 4.0 15.2 1.0
N A:VAL746 4.2 14.2 1.0
C14 A:97A1004 4.3 17.8 0.5
C14 A:97A1004 4.3 16.2 0.5
CB A:MET745 4.3 16.4 1.0
SD A:MET749 4.5 17.6 1.0
CG2 A:VAL746 4.6 15.5 0.3
CB A:VAL746 4.6 17.7 0.7
CG2 A:VAL746 4.7 18.4 0.7
C12 A:97A1004 4.7 18.1 0.5
CA A:MET749 4.8 14.3 1.0
C12 A:97A1004 4.8 18.3 0.5
CA A:MET745 4.8 15.1 1.0
O A:HOH1195 4.8 17.2 1.0
SD A:MET787 4.8 23.4 1.0
CB A:VAL746 4.9 15.8 0.3
CG A:PHE764 4.9 15.1 1.0
CZ A:PHE764 4.9 16.6 1.0
NH2 A:ARG752 5.0 16.2 1.0
C A:VAL746 5.0 14.9 1.0

Fluorine binding site 6 out of 6 in 5v8q

Go back to Fluorine Binding Sites List in 5v8q
Fluorine binding site 6 out of 6 in the Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms): Part III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:19.6
occ:0.50
F23 A:97A1004 0.0 19.6 0.5
F23 A:97A1004 0.5 18.3 0.5
C20 A:97A1004 1.4 18.4 0.5
C20 A:97A1004 1.5 18.3 0.5
F21 A:97A1004 2.1 18.3 0.5
F22 A:97A1004 2.3 18.8 0.5
F21 A:97A1004 2.3 17.4 0.5
C18 A:97A1004 2.4 17.2 0.5
C18 A:97A1004 2.5 17.5 0.5
F22 A:97A1004 2.6 17.9 0.5
C16 A:97A1004 2.8 18.0 0.5
C16 A:97A1004 2.9 20.0 0.5
C15 A:97A1004 3.0 17.9 0.5
C15 A:97A1004 3.0 17.8 0.5
CE1 A:PHE764 3.2 16.7 1.0
N17 A:97A1004 3.2 19.7 0.5
CD1 A:PHE764 3.2 15.2 1.0
N17 A:97A1004 3.3 23.4 0.5
CB A:MET749 3.4 15.4 1.0
CG A:MET749 3.4 16.5 1.0
CE A:MET749 3.4 18.8 1.0
C19 A:97A1004 3.5 17.9 0.5
C19 A:97A1004 3.6 18.1 0.5
O A:MET745 4.1 16.3 1.0
SD A:MET749 4.2 17.6 1.0
C14 A:97A1004 4.3 17.8 0.5
CA A:VAL746 4.3 15.2 1.0
C14 A:97A1004 4.3 16.2 0.5
CZ A:PHE764 4.4 16.6 1.0
C A:MET745 4.5 14.5 1.0
CG A:PHE764 4.5 15.1 1.0
SD A:MET787 4.6 23.4 1.0
N A:VAL746 4.6 14.2 1.0
C12 A:97A1004 4.7 18.1 0.5
C12 A:97A1004 4.8 18.3 0.5
CG2 A:VAL746 4.8 18.4 0.7
CG2 A:VAL746 4.8 15.5 0.3
CB A:MET745 4.9 16.4 1.0
CB A:VAL746 4.9 17.7 0.7
CA A:MET749 4.9 14.3 1.0

Reference:

K.Aikawa, M.Asano, K.Ono, N.Habuka, J.Yano, K.Wilson, H.Fujita, H.Kandori, T.Hara, M.Morimoto, T.Santou, M.Yamaoka, M.Nakayama, A.Hasuoka. Synthesis and Biological Evaluation of Novel Selective Androgen Receptor Modulators (Sarms) Part III: Discovery of 4-(5-Oxopyrrolidine-1-Yl)Benzonitrile Derivative 2F As A Clinical Candidate. Bioorg. Med. Chem. V. 25 3330 2017.
ISSN: ESSN 1464-3391
PubMed: 28454849
DOI: 10.1016/J.BMC.2017.04.018
Page generated: Tue Jul 15 08:30:37 2025

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