Fluorine in PDB 6kgp: LSD1-S2157 N5 Adduct Model

The structure of LSD1-S2157 N5 Adduct Model, PDB code: 6kgp was solved by H.Niwa, S.Sato, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.60 / 2.25
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	185.703, 185.703, 108.500, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 20.4

The binding sites of Fluorine atom in the LSD1-S2157 N5 Adduct Model (pdb code 6kgp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the LSD1-S2157 N5 Adduct Model, PDB code: 6kgp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-S2157 N5 Adduct Model


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of LSD1-S2157 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F908 b:74.1 occ:1.00 F A:DJ0908 0.0 74.1 1.0 C32 A:DJ0908 1.4 74.9 1.0 C33 A:DJ0908 2.3 71.3 1.0 C31 A:DJ0908 2.4 66.1 1.0 O16 A:DJ0908 2.8 65.5 1.0 C36 A:DJ0908 2.9 65.5 1.0 C42 A:DJ0908 3.0 70.3 1.0 C37 A:DJ0908 3.1 72.2 1.0 CG2 A:THR335 3.2 41.6 1.0 C34 A:DJ0908 3.6 69.2 1.0 C30 A:DJ0908 3.6 65.8 1.0 C35 A:DJ0908 4.1 67.8 1.0 C41 A:DJ0908 4.1 68.6 1.0 CG2 A:THR810 4.3 36.4 1.0 C38 A:DJ0908 4.3 76.8 1.0 CB A:THR335 4.6 50.8 1.0 F1 A:DJ0908 4.7 77.0 1.0 C29 A:DJ0908 4.9 60.7 1.0

Fluorine binding site 2 out of 2 in the LSD1-S2157 N5 Adduct Model


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of LSD1-S2157 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F908 b:77.0 occ:1.00 F1 A:DJ0908 0.0 77.0 1.0 C34 A:DJ0908 1.4 69.2 1.0 C33 A:DJ0908 2.3 71.3 1.0 C35 A:DJ0908 2.3 67.8 1.0 CB A:ALA809 3.2 37.4 1.0 O A:ALA809 3.4 45.9 1.0 C32 A:DJ0908 3.6 74.9 1.0 C30 A:DJ0908 3.6 65.8 1.0 O A:PRO808 3.7 41.7 1.0 C A:ALA809 3.9 39.4 1.0 CG2 A:THR810 4.0 36.4 1.0 C31 A:DJ0908 4.1 66.1 1.0 O A:HOH1063 4.1 50.8 1.0 CA A:ALA809 4.1 37.8 1.0 O A:ALA539 4.3 56.8 1.0 O A:HOH1059 4.4 46.0 1.0 CE1 A:TYR761 4.5 39.4 1.0 CD1 A:TYR761 4.6 45.8 1.0 C A:PRO808 4.6 37.2 1.0 F A:DJ0908 4.7 74.1 1.0 C29 A:DJ0908 4.8 60.7 1.0 N A:THR810 4.8 36.7 1.0 N A:ALA809 4.9 38.2 1.0

H.Niwa, S.Sato, N.Handa, T.Sengoku, T.Umehara, S.Yokoyama. Development and Structural Evaluation of N-Alkylated Trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors. Chemmedchem 2020.
ISSN: ESSN 1860-7187
PubMed: 32166890
DOI: 10.1002/CMDC.202000014