Fluorine in PDB 7vqs: Crystal Structure of LSD1 in Complex with Compound 4

All present enzymatic activity of Crystal Structure of LSD1 in Complex with Compound 4:
1.14.99.66;

The structure of Crystal Structure of LSD1 in Complex with Compound 4, PDB code: 7vqs was solved by H.Niwa, Y.Koda, S.Sato, H.Yamamoto, H.Koyama, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 2.94
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	186.245, 186.245, 106.553, 90, 90, 120
R / Rfree (%)	21.3 / 25.6

The binding sites of Fluorine atom in the Crystal Structure of LSD1 in Complex with Compound 4 (pdb code 7vqs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of LSD1 in Complex with Compound 4, PDB code: 7vqs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of LSD1 in Complex with Compound 4


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 LSD1 in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:87.7 occ:1.00 F A:7UQ906 0.0 87.7 1.0 C19 A:7UQ906 1.3 88.1 1.0 N4 A:7UQ906 2.2 88.8 1.0 C18 A:7UQ906 2.3 87.3 1.0 NZ A:LYS661 2.6 73.6 1.0 C17 A:7UQ906 2.9 81.9 1.0 CE A:LYS661 3.2 73.7 1.0 O3 A:7UQ906 3.4 77.4 1.0 C20 A:7UQ906 3.5 93.3 1.0 C12 A:7UQ906 3.5 70.6 1.0 C22 A:7UQ906 3.6 93.9 1.0 O A:GLY330 3.6 66.7 1.0 C6 A:FAD907 3.6 65.4 1.0 CG A:MET332 3.7 77.3 1.0 N5 A:FAD907 3.8 68.9 1.0 SD A:MET332 4.0 89.0 1.0 C21 A:7UQ906 4.0 96.4 1.0 C5X A:FAD907 4.2 63.7 1.0 O4 A:FAD907 4.2 67.0 1.0 CB A:MET332 4.3 75.2 1.0 C16 A:7UQ906 4.4 74.8 1.0 CD A:LYS661 4.4 77.5 1.0 C13 A:7UQ906 4.4 76.9 1.0 C15 A:7UQ906 4.5 71.4 1.0 N A:MET332 4.6 72.6 1.0 C4X A:FAD907 4.7 66.2 1.0 C A:GLY330 4.7 68.1 1.0 C7 A:FAD907 4.7 64.1 1.0 C4 A:FAD907 4.8 66.8 1.0 CE1 A:PHE538 4.9 83.3 1.0 CA A:ALA331 4.9 66.5 1.0 C7M A:FAD907 4.9 68.2 1.0 C A:ALA331 4.9 71.0 1.0 CA A:MET332 5.0 71.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of LSD1 in Complex with Compound 4


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 LSD1 in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:75.7 occ:1.00 F1 A:7UQ906 0.0 75.7 1.0 C23 A:7UQ906 1.3 71.3 1.0 C24 A:7UQ906 2.3 68.3 1.0 C16 A:7UQ906 2.3 74.8 1.0 O3 A:7UQ906 2.8 77.4 1.0 C17 A:7UQ906 3.1 81.9 1.0 C25 A:7UQ906 3.6 68.5 1.0 C15 A:7UQ906 3.6 71.4 1.0 CB A:VAL333 3.7 72.9 1.0 CG1 A:VAL333 3.7 71.3 1.0 CG2 A:VAL333 3.8 75.5 1.0 C26 A:7UQ906 4.1 68.8 1.0 C18 A:7UQ906 4.3 87.3 1.0 O2 A:7UQ906 4.5 88.1 1.0 O4 A:FAD907 4.6 67.0 1.0 F2 A:7UQ906 4.6 77.8 1.0 C22 A:7UQ906 4.7 93.9 1.0 C12 A:7UQ906 4.8 70.6 1.0 CD2 A:HIS564 4.9 73.6 1.0 CZ A:PHE538 5.0 86.6 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of LSD1 in Complex with Compound 4


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 LSD1 in Complex with Compound 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:77.8 occ:1.00 F2 A:7UQ906 0.0 77.8 1.0 C25 A:7UQ906 1.3 68.5 1.0 C24 A:7UQ906 2.3 68.3 1.0 C26 A:7UQ906 2.3 68.8 1.0 CG2 A:THR810 3.5 74.9 1.0 C23 A:7UQ906 3.5 71.3 1.0 C15 A:7UQ906 3.6 71.4 1.0 C2 A:FAD907 4.0 61.6 1.0 N3 A:FAD907 4.0 63.0 1.0 O A:ALA809 4.1 73.0 1.0 C16 A:7UQ906 4.1 74.8 1.0 O2 A:FAD907 4.1 65.1 1.0 CG2 A:THR335 4.2 67.5 1.0 N1 A:FAD907 4.3 61.2 1.0 CB A:THR810 4.4 71.8 1.0 C4 A:FAD907 4.5 66.8 1.0 F1 A:7UQ906 4.6 75.7 1.0 C4X A:FAD907 4.7 66.2 1.0 CA A:THR810 4.8 72.7 1.0 C10 A:FAD907 4.8 63.0 1.0 C14 A:7UQ906 4.9 85.2 1.0 C12 A:7UQ906 4.9 70.6 1.0

Y.Koda, S.Sato, H.Yamamoto, H.Niwa, H.Watanabe, C.Watanabe, T.Sato, K.Nakamura, A.Tanaka, M.Shirouzu, T.Honma, T.Fukami, H.Koyama, T.Umehara. Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved Herg and Microsomal Stability Profiles. Acs Med.Chem.Lett. V. 13 848 2022.
ISSN: ISSN 1948-5875
PubMed: 35586426
DOI: 10.1021/ACSMEDCHEMLETT.2C00120