Fluorine in PDB 6kgn: LSD1-Corest-S2116 N5 Adduct Model

The structure of LSD1-Corest-S2116 N5 Adduct Model, PDB code: 6kgn 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 (%)	17.5 / 19.4

The binding sites of Fluorine atom in the LSD1-Corest-S2116 N5 Adduct Model (pdb code 6kgn). 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 N5 Adduct Model, PDB code: 6kgn:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-Corest-S2116 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-Corest-S2116 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:0.7 occ:1.00 F A:DJ0906 0.0 0.7 1.0 C32 A:DJ0906 1.3 0.2 1.0 C33 A:DJ0906 2.3 0.6 1.0 C31 A:DJ0906 2.4 0.1 1.0 O16 A:DJ0906 2.8 0.9 1.0 C36 A:DJ0906 2.9 0.3 1.0 CG2 A:THR335 3.0 73.1 1.0 C42 A:DJ0906 3.1 0.9 1.0 C37 A:DJ0906 3.3 0.1 1.0 C34 A:DJ0906 3.6 0.3 1.0 C30 A:DJ0906 3.6 94.2 1.0 C35 A:DJ0906 4.1 99.7 1.0 CG2 A:THR810 4.1 49.1 1.0 C41 A:DJ0906 4.2 0.7 1.0 CB A:THR335 4.4 77.5 1.0 C38 A:DJ0906 4.5 0.1 1.0 F1 A:DJ0906 4.7 0.8 1.0 C29 A:DJ0906 4.9 81.0 1.0 O2 A:FAD907 5.0 69.0 1.0 C2 A:FAD907 5.0 65.3 1.0

Fluorine binding site 2 out of 2 in the LSD1-Corest-S2116 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-Corest-S2116 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F906 b:0.8 occ:1.00 F1 A:DJ0906 0.0 0.8 1.0 C34 A:DJ0906 1.4 0.3 1.0 C33 A:DJ0906 2.3 0.6 1.0 C35 A:DJ0906 2.3 99.7 1.0 CB A:ALA809 3.3 38.3 1.0 C32 A:DJ0906 3.6 0.2 1.0 O A:ALA809 3.6 62.2 1.0 C30 A:DJ0906 3.6 94.2 1.0 O A:PRO808 3.7 53.2 1.0 O A:HOH1054 3.7 88.5 1.0 C A:ALA809 4.0 55.8 1.0 O A:HOH1003 4.1 60.9 1.0 C31 A:DJ0906 4.1 0.1 1.0 CG2 A:THR810 4.1 49.1 1.0 CA A:ALA809 4.3 53.9 1.0 O A:ALA539 4.3 71.0 1.0 CE2 A:TYR761 4.4 61.8 1.0 CD2 A:TYR761 4.6 62.1 1.0 C A:PRO808 4.7 55.0 1.0 F A:DJ0906 4.7 0.7 1.0 C29 A:DJ0906 4.8 81.0 1.0 N A:THR810 4.9 54.2 1.0 N A:ALA809 5.0 53.6 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