Fluorine in PDB 6kgm: LSD1-Corest-S2116 Five-Membered Ring Adduct Model

The structure of LSD1-Corest-S2116 Five-Membered Ring Adduct Model, PDB code: 6kgm 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)	49.13 / 2.62
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.451, 178.696, 235.256, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 19.5

The binding sites of Fluorine atom in the LSD1-Corest-S2116 Five-Membered Ring Adduct Model (pdb code 6kgm). 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-Corest-S2116 Five-Membered Ring Adduct Model, PDB code: 6kgm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-Corest-S2116 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-Corest-S2116 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:0.9 occ:1.00 F A:DJ0906 0.0 0.9 1.0 C32 A:DJ0906 1.3 0.2 1.0 C33 A:DJ0906 2.3 0.5 1.0 C31 A:DJ0906 2.4 0.5 1.0 O16 A:DJ0906 2.8 0.2 1.0 C36 A:DJ0906 2.8 0.7 1.0 CG2 A:THR335 2.9 73.2 1.0 C42 A:DJ0906 3.0 1.0 1.0 C37 A:DJ0906 3.1 0.6 1.0 C34 A:DJ0906 3.6 97.9 1.0 C30 A:DJ0906 3.6 90.6 1.0 C35 A:DJ0906 4.1 96.7 1.0 C41 A:DJ0906 4.1 0.7 1.0 CB A:THR335 4.4 76.9 1.0 C38 A:DJ0906 4.4 0.7 1.0 CG2 A:THR810 4.5 50.2 1.0 F1 A:DJ0906 4.7 94.3 1.0 C29 A:DJ0906 4.9 82.4 1.0

Fluorine binding site 2 out of 2 in the LSD1-Corest-S2116 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-Corest-S2116 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:94.3 occ:1.00 F1 A:DJ0906 0.0 94.3 1.0 C34 A:DJ0906 1.4 97.9 1.0 C33 A:DJ0906 2.3 0.5 1.0 C35 A:DJ0906 2.4 96.7 1.0 O A:ALA809 3.3 62.4 1.0 CB A:ALA809 3.4 38.7 1.0 C32 A:DJ0906 3.6 0.2 1.0 C30 A:DJ0906 3.6 90.6 1.0 C A:ALA809 3.9 56.3 1.0 O A:PRO808 3.9 53.9 1.0 CG2 A:THR810 4.0 50.2 1.0 O A:HOH1054 4.0 88.2 1.0 C31 A:DJ0906 4.1 0.5 1.0 O A:ALA539 4.2 70.9 1.0 CE2 A:TYR761 4.2 63.9 1.0 CA A:ALA809 4.3 53.8 1.0 O A:HOH1003 4.4 59.7 1.0 CD2 A:TYR761 4.5 62.4 1.0 F A:DJ0906 4.7 0.9 1.0 N A:THR810 4.8 53.9 1.0 C A:PRO808 4.9 55.2 1.0 C29 A:DJ0906 4.9 82.4 1.0 CZ A:TYR761 4.9 69.5 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