Fluorine in PDB 7vqt: Crystal Structure of LSD1 in Complex with Compound 5

All present enzymatic activity of Crystal Structure of LSD1 in Complex with Compound 5:
1.14.99.66;

The structure of Crystal Structure of LSD1 in Complex with Compound 5, PDB code: 7vqt 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)	47.83 / 2.91
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	185.256, 185.256, 106.881, 90, 90, 120
R / Rfree (%)	20.9 / 25.8

The binding sites of Fluorine atom in the Crystal Structure of LSD1 in Complex with Compound 5 (pdb code 7vqt). 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 5, PDB code: 7vqt:
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 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:80.6 occ:1.00 F A:7UW906 0.0 80.6 1.0 C21 A:7UW906 1.4 77.7 1.0 NZ A:LYS661 2.0 82.5 1.0 N4 A:7UW906 2.2 77.8 1.0 C22 A:7UW906 2.3 70.3 1.0 CE A:LYS661 2.8 81.1 1.0 CD A:LYS661 3.1 77.3 1.0 O A:GLY330 3.3 61.2 1.0 C20 A:7UW906 3.4 79.0 1.0 C18 A:7UW906 3.6 76.3 1.0 CB A:MET332 3.6 67.8 1.0 SD A:MET332 3.7 71.7 1.0 C19 A:7UW906 4.0 80.2 1.0 CG A:MET332 4.1 67.2 1.0 O A:ASP328 4.2 78.1 1.0 CG A:LYS661 4.2 81.0 1.0 C A:GLY330 4.5 65.5 1.0 C6 A:FAD907 4.8 63.5 1.0 CD1 A:LEU704 4.8 84.7 1.0 C17 A:7UW906 4.8 80.9 1.0 CD2 A:LEU706 4.9 79.3 1.0 CA A:MET332 5.0 69.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of LSD1 in Complex with Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:82.9 occ:1.00 F1 A:7UW906 0.0 82.9 1.0 C23 A:7UW906 1.3 73.6 1.0 C24 A:7UW906 2.3 69.1 1.0 C16 A:7UW906 2.3 74.0 1.0 O3 A:7UW906 2.7 78.8 1.0 C17 A:7UW906 3.1 80.9 1.0 C25 A:7UW906 3.6 68.5 1.0 C15 A:7UW906 3.6 71.8 1.0 CB A:VAL333 4.0 71.1 1.0 CG1 A:VAL333 4.0 72.1 1.0 C26 A:7UW906 4.1 67.9 1.0 CG2 A:VAL333 4.1 72.4 1.0 O2 A:7UW906 4.2 81.9 1.0 C18 A:7UW906 4.5 76.3 1.0 F2 A:7UW906 4.7 72.9 1.0 CZ A:PHE538 4.8 78.5 1.0 C12 A:7UW906 4.8 77.7 1.0 CD2 A:HIS564 4.8 72.6 1.0 C14 A:7UW906 4.8 79.8 1.0 O4 A:FAD907 4.9 68.8 1.0 C19 A:7UW906 5.0 80.2 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of LSD1 in Complex with Compound 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:72.9 occ:1.00 F2 A:7UW906 0.0 72.9 1.0 C25 A:7UW906 1.4 68.5 1.0 C24 A:7UW906 2.3 69.1 1.0 C26 A:7UW906 2.3 67.9 1.0 CG2 A:THR810 3.5 70.6 1.0 C23 A:7UW906 3.5 73.6 1.0 C15 A:7UW906 3.6 71.8 1.0 C2 A:FAD907 3.8 65.1 1.0 N3 A:FAD907 4.0 66.3 1.0 O2 A:FAD907 4.0 63.4 1.0 O A:ALA809 4.1 70.7 1.0 C16 A:7UW906 4.1 74.0 1.0 CG2 A:THR335 4.1 66.6 1.0 N1 A:FAD907 4.1 63.0 1.0 CB A:THR810 4.3 72.5 1.0 C4 A:FAD907 4.3 66.7 1.0 C4X A:FAD907 4.4 65.8 1.0 C10 A:FAD907 4.6 64.4 1.0 CA A:THR810 4.6 68.7 1.0 F1 A:7UW906 4.7 82.9 1.0 C12 A:7UW906 4.9 77.7 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