Fluorine in PDB 6kgl: LSD1-Corest-S2101 N5 Adduct Model

The structure of LSD1-Corest-S2101 N5 Adduct Model, PDB code: 6kgl 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 / 20.5

The binding sites of Fluorine atom in the LSD1-Corest-S2101 N5 Adduct Model (pdb code 6kgl). 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 N5 Adduct Model, PDB code: 6kgl:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the LSD1-Corest-S2101 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-S2101 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F904 b:0.5 occ:1.00 F A:DJ0904 0.0 0.5 1.0 C32 A:DJ0904 1.3 0.9 1.0 C33 A:DJ0904 2.3 0.1 1.0 C31 A:DJ0904 2.3 97.3 1.0 O16 A:DJ0904 2.8 0.3 1.0 C36 A:DJ0904 2.8 96.6 1.0 C42 A:DJ0904 3.1 95.1 1.0 CG2 A:THR335 3.1 60.7 1.0 C37 A:DJ0904 3.2 95.8 1.0 C34 A:DJ0904 3.6 94.2 1.0 C30 A:DJ0904 3.6 85.6 1.0 C35 A:DJ0904 4.1 96.3 1.0 C41 A:DJ0904 4.2 86.5 1.0 CG2 A:THR810 4.3 49.1 1.0 C38 A:DJ0904 4.3 94.0 1.0 CB A:THR335 4.5 65.0 1.0 F1 A:DJ0904 4.7 83.0 1.0 C29 A:DJ0904 4.9 73.7 1.0

Fluorine binding site 2 out of 2 in the LSD1-Corest-S2101 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-S2101 N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F904 b:83.0 occ:1.00 F1 A:DJ0904 0.0 83.0 1.0 C34 A:DJ0904 1.4 94.2 1.0 C33 A:DJ0904 2.3 0.1 1.0 C35 A:DJ0904 2.3 96.3 1.0 CB A:ALA809 3.2 36.5 1.0 O A:ALA809 3.5 59.2 1.0 C32 A:DJ0904 3.6 0.9 1.0 C30 A:DJ0904 3.6 85.6 1.0 O A:PRO808 3.8 50.8 1.0 C A:ALA809 3.9 55.6 1.0 CG2 A:THR810 4.0 49.1 1.0 C31 A:DJ0904 4.1 97.3 1.0 CA A:ALA809 4.2 55.1 1.0 O A:HOH1004 4.2 56.9 1.0 O A:ALA539 4.2 72.6 1.0 CE2 A:TYR761 4.4 60.1 1.0 CD2 A:TYR761 4.6 58.9 1.0 C A:PRO808 4.7 53.5 1.0 F A:DJ0904 4.7 0.5 1.0 N A:THR810 4.8 51.1 1.0 C29 A:DJ0904 4.8 73.7 1.0 N A:ALA809 4.9 53.8 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