Fluorine in PDB 6kgk: LSD1-Corest-S2101 Five-Membered Ring Adduct Model

The structure of LSD1-Corest-S2101 Five-Membered Ring Adduct Model, PDB code: 6kgk was solved by H.Niwa, S.Sato, S.Sengoku, T.Umehara, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.96 / 2.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.545, 178.549, 234.194, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.6

The binding sites of Fluorine atom in the LSD1-Corest-S2101 Five-Membered Ring Adduct Model (pdb code 6kgk). 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-S2101 Five-Membered Ring Adduct Model, PDB code: 6kgk:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-Corest-S2101 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-S2101 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F904 b:84.9 occ:1.00 F A:DJ0904 0.0 84.9 1.0 C32 A:DJ0904 1.3 82.5 1.0 C33 A:DJ0904 2.3 74.8 1.0 C31 A:DJ0904 2.4 83.1 1.0 C36 A:DJ0904 2.8 86.0 1.0 O16 A:DJ0904 2.8 93.5 1.0 CG2 A:THR335 3.0 63.8 1.0 C42 A:DJ0904 3.0 86.2 1.0 C37 A:DJ0904 3.1 88.7 1.0 C34 A:DJ0904 3.5 75.1 1.0 C30 A:DJ0904 3.6 71.2 1.0 C35 A:DJ0904 4.1 73.9 1.0 C41 A:DJ0904 4.2 79.3 1.0 C38 A:DJ0904 4.2 89.7 1.0 CB A:THR335 4.5 68.5 1.0 CG2 A:THR810 4.5 53.5 1.0 F1 A:DJ0904 4.7 65.2 1.0 C29 A:DJ0904 4.9 74.5 1.0

Fluorine binding site 2 out of 2 in the LSD1-Corest-S2101 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-S2101 Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F904 b:65.2 occ:1.00 F1 A:DJ0904 0.0 65.2 1.0 C34 A:DJ0904 1.4 75.1 1.0 C33 A:DJ0904 2.3 74.8 1.0 C35 A:DJ0904 2.4 73.9 1.0 O A:ALA809 3.3 58.9 1.0 CB A:ALA809 3.3 35.9 1.0 C32 A:DJ0904 3.6 82.5 1.0 C30 A:DJ0904 3.7 71.2 1.0 C A:ALA809 3.9 59.0 1.0 CG2 A:THR810 3.9 53.5 1.0 O A:PRO808 4.0 52.0 1.0 C31 A:DJ0904 4.1 83.1 1.0 O A:ALA539 4.1 74.6 1.0 CA A:ALA809 4.2 59.5 1.0 CE2 A:TYR761 4.3 63.9 1.0 CD2 A:TYR761 4.5 57.9 1.0 O A:HOH1104 4.5 57.4 1.0 F A:DJ0904 4.7 84.9 1.0 N A:THR810 4.8 52.6 1.0 C A:PRO808 4.9 53.4 1.0 C29 A:DJ0904 4.9 74.5 1.0 CZ A:TYR761 5.0 71.0 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