Fluorine in PDB 7vqu: Crystal Structure of LSD1 in Complex with Compound S1427

All present enzymatic activity of Crystal Structure of LSD1 in Complex with Compound S1427:
1.14.99.66;

The structure of Crystal Structure of LSD1 in Complex with Compound S1427, PDB code: 7vqu 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)	48.45 / 2.94
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	188.248, 188.248, 106.997, 90, 90, 120
R / Rfree (%)	21.9 / 25.8

The binding sites of Fluorine atom in the Crystal Structure of LSD1 in Complex with Compound S1427 (pdb code 7vqu). 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 S1427, PDB code: 7vqu:
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 S1427


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 S1427 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:97.0 occ:1.00 F A:7UQ906 0.0 97.0 1.0 C19 A:7UQ906 1.3 95.4 1.0 N4 A:7UQ906 2.2 95.6 1.0 C18 A:7UQ906 2.3 99.0 1.0 C17 A:7UQ906 2.8 91.7 1.0 NZ A:LYS661 3.0 89.9 1.0 O3 A:7UQ906 3.2 84.0 1.0 C12 A:7UQ906 3.3 81.8 1.0 CE A:LYS661 3.4 85.6 1.0 C20 A:7UQ906 3.4 102.0 1.0 C6 A:FAD907 3.5 74.4 1.0 C22 A:7UQ906 3.6 105.5 1.0 N5 A:FAD907 3.6 78.9 1.0 O A:GLY330 3.8 78.0 1.0 C5X A:FAD907 4.0 73.8 1.0 C21 A:7UQ906 4.0 108.0 1.0 C16 A:7UQ906 4.1 82.9 1.0 O4 A:FAD907 4.1 74.3 1.0 C13 A:7UQ906 4.2 89.1 1.0 C15 A:7UQ906 4.3 79.5 1.0 CB A:MET332 4.3 86.8 1.0 SD A:MET332 4.3 96.3 1.0 CG A:MET332 4.5 89.1 1.0 C4X A:FAD907 4.5 77.7 1.0 CE1 A:PHE538 4.7 99.3 1.0 C7 A:FAD907 4.7 72.9 1.0 CD A:LYS661 4.7 88.1 1.0 C4 A:FAD907 4.7 76.2 1.0 C A:GLY330 4.8 83.3 1.0 N A:MET332 4.8 88.5 1.0 C7M A:FAD907 4.9 77.7 1.0 CA A:ALA331 5.0 81.6 1.0 CZ A:PHE538 5.0 101.7 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of LSD1 in Complex with Compound S1427


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 S1427 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:86.2 occ:1.00 F1 A:7UQ906 0.0 86.2 1.0 C23 A:7UQ906 1.3 81.8 1.0 C24 A:7UQ906 2.3 77.0 1.0 C16 A:7UQ906 2.3 82.9 1.0 O3 A:7UQ906 2.7 84.0 1.0 C17 A:7UQ906 2.9 91.7 1.0 CB A:VAL333 3.5 79.5 1.0 C25 A:7UQ906 3.6 78.2 1.0 C15 A:7UQ906 3.6 79.5 1.0 CG2 A:VAL333 3.6 84.3 1.0 CG1 A:VAL333 3.8 78.9 1.0 C26 A:7UQ906 4.1 76.7 1.0 C18 A:7UQ906 4.2 99.0 1.0 O4 A:FAD907 4.6 74.3 1.0 C22 A:7UQ906 4.6 105.5 1.0 F2 A:7UQ906 4.6 93.4 1.0 CD2 A:HIS564 4.8 87.6 1.0 C12 A:7UQ906 4.8 81.8 1.0 CZ A:PHE538 4.9 101.7 1.0 O2 A:7UQ906 4.9 96.8 1.0 CA A:VAL333 4.9 87.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of LSD1 in Complex with Compound S1427


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 S1427 within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:93.4 occ:1.00 F2 A:7UQ906 0.0 93.4 1.0 C25 A:7UQ906 1.3 78.2 1.0 C24 A:7UQ906 2.3 77.0 1.0 C26 A:7UQ906 2.3 76.7 1.0 C23 A:7UQ906 3.5 81.8 1.0 CG2 A:THR810 3.6 89.9 1.0 C15 A:7UQ906 3.6 79.5 1.0 C2 A:FAD907 4.0 73.4 1.0 C16 A:7UQ906 4.1 82.9 1.0 N3 A:FAD907 4.1 73.8 1.0 O A:ALA809 4.2 96.0 1.0 O2 A:FAD907 4.2 79.3 1.0 CG2 A:THR335 4.3 80.2 1.0 N1 A:FAD907 4.3 74.5 1.0 CB A:THR810 4.5 87.0 1.0 C4 A:FAD907 4.6 76.2 1.0 F1 A:7UQ906 4.6 86.2 1.0 C4X A:FAD907 4.7 77.7 1.0 C10 A:FAD907 4.8 74.2 1.0 CA A:THR810 4.8 87.5 1.0 C12 A:7UQ906 4.9 81.8 1.0 C14 A:7UQ906 5.0 94.0 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