Fluorine in PDB 6kgo: LSD1-S2157 Five-Membered Ring Adduct Model

The structure of LSD1-S2157 Five-Membered Ring Adduct Model, PDB code: 6kgo 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 Five-Membered Ring Adduct Model (pdb code 6kgo). 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 Five-Membered Ring Adduct Model, PDB code: 6kgo:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-S2157 Five-Membered Ring 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 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F908 b:74.5 occ:1.00 F A:DJ0908 0.0 74.5 1.0 C32 A:DJ0908 1.4 74.6 1.0 C33 A:DJ0908 2.3 71.1 1.0 C31 A:DJ0908 2.4 66.2 1.0 C36 A:DJ0908 2.8 68.5 1.0 O16 A:DJ0908 2.8 68.1 1.0 C42 A:DJ0908 3.0 71.2 1.0 C37 A:DJ0908 3.1 73.7 1.0 CG2 A:THR335 3.2 42.5 1.0 C34 A:DJ0908 3.6 68.3 1.0 C30 A:DJ0908 3.6 64.3 1.0 C41 A:DJ0908 4.1 69.7 1.0 C35 A:DJ0908 4.1 69.3 1.0 C38 A:DJ0908 4.2 78.0 1.0 CG2 A:THR810 4.5 36.8 1.0 F1 A:DJ0908 4.7 71.7 1.0 CB A:THR335 4.7 51.3 1.0 C29 A:DJ0908 4.9 64.7 1.0 CE1 A:HIS564 5.0 54.7 1.0 C40 A:DJ0908 5.0 72.5 1.0

Fluorine binding site 2 out of 2 in the LSD1-S2157 Five-Membered Ring 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 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F908 b:71.7 occ:1.00 F1 A:DJ0908 0.0 71.7 1.0 C34 A:DJ0908 1.4 68.3 1.0 C33 A:DJ0908 2.3 71.1 1.0 C35 A:DJ0908 2.4 69.3 1.0 O A:ALA809 3.1 45.6 1.0 CB A:ALA809 3.2 37.5 1.0 C32 A:DJ0908 3.6 74.6 1.0 C30 A:DJ0908 3.6 64.3 1.0 C A:ALA809 3.8 40.2 1.0 O A:PRO808 4.0 42.5 1.0 CG2 A:THR810 4.0 36.8 1.0 C31 A:DJ0908 4.1 66.2 1.0 CA A:ALA809 4.1 38.2 1.0 O A:ALA539 4.2 57.3 1.0 CE1 A:TYR761 4.2 40.3 1.0 CD1 A:TYR761 4.3 46.8 1.0 O A:HOH1060 4.5 47.3 1.0 O A:HOH1059 4.5 52.5 1.0 F A:DJ0908 4.7 74.5 1.0 N A:THR810 4.8 37.3 1.0 C A:PRO808 4.8 37.8 1.0 CZ A:TYR761 4.9 49.5 1.0 C29 A:DJ0908 4.9 64.7 1.0 N A:ALA809 5.0 38.7 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