Fluorine in PDB 6kgr: LSD1-Fcpa-Mpe N5 Adduct Model

The structure of LSD1-Fcpa-Mpe N5 Adduct Model, PDB code: 6kgr was solved by H.Niwa, S.Sato, N.Handa, T.Umehara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.88 / 2.32
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	185.268, 185.268, 109.327, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 19.8

The binding sites of Fluorine atom in the LSD1-Fcpa-Mpe N5 Adduct Model (pdb code 6kgr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the LSD1-Fcpa-Mpe N5 Adduct Model, PDB code: 6kgr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the LSD1-Fcpa-Mpe 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-Fcpa-Mpe N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:78.4 occ:1.00 F A:DJC902 0.0 78.4 1.0 C40 A:DJC902 1.4 67.3 1.0 C39 A:DJC902 2.3 58.0 1.0 C41 A:DJC902 2.3 62.2 1.0 O A:HOH1243 2.6 51.6 1.0 O A:HOH1213 2.9 57.6 1.0 O A:HOH1146 3.4 52.5 1.0 O A:HOH1153 3.6 44.2 1.0 C38 A:DJC902 3.6 55.9 1.0 C36 A:DJC902 3.6 61.3 1.0 CG A:GLU559 3.6 91.4 1.0 C37 A:DJC902 4.1 65.2 1.0 OD2 A:ASP555 4.1 73.0 1.0 CD A:GLU559 4.4 95.9 1.0 CA A:GLU559 4.5 68.3 1.0 CB A:GLU559 4.5 76.9 1.0 OE2 A:GLU559 4.6 97.2 1.0 C33 A:DJC902 4.8 64.4 1.0

Fluorine binding site 2 out of 4 in the LSD1-Fcpa-Mpe 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-Fcpa-Mpe N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:74.1 occ:1.00 F1 A:DJC902 0.0 74.1 1.0 C42 A:DJC902 1.3 72.9 1.0 F3 A:DJC902 2.1 74.3 1.0 F2 A:DJC902 2.1 75.8 1.0 C37 A:DJC902 2.4 65.2 1.0 C32 A:DJC902 3.0 63.7 1.0 C36 A:DJC902 3.1 61.3 1.0 C1 A:MPD901 3.1 77.5 1.0 C33 A:DJC902 3.2 64.4 1.0 CE1 A:HIS564 3.3 64.7 1.0 C38 A:DJC902 3.4 55.9 1.0 ND1 A:HIS564 3.6 64.6 1.0 C31 A:DJC902 3.9 63.3 1.0 C34 A:DJC902 4.3 71.8 1.0 C41 A:DJC902 4.4 62.2 1.0 NE2 A:HIS564 4.4 63.6 1.0 C2 A:MPD901 4.4 77.1 1.0 CG2 A:THR335 4.4 47.3 1.0 CM A:MPD901 4.6 73.0 1.0 C39 A:DJC902 4.6 58.0 1.0 C30 A:DJC902 4.7 68.7 1.0 CG A:HIS564 4.8 63.3 1.0 O2 A:MPD901 4.8 79.2 1.0 CG1 A:VAL333 4.9 44.5 1.0 C35 A:DJC902 4.9 73.4 1.0 C40 A:DJC902 4.9 67.3 1.0

Fluorine binding site 3 out of 4 in the LSD1-Fcpa-Mpe N5 Adduct Model


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of LSD1-Fcpa-Mpe N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:75.8 occ:1.00 F2 A:DJC902 0.0 75.8 1.0 C42 A:DJC902 1.3 72.9 1.0 F1 A:DJC902 2.1 74.1 1.0 F3 A:DJC902 2.1 74.3 1.0 C37 A:DJC902 2.4 65.2 1.0 C33 A:DJC902 2.9 64.4 1.0 C36 A:DJC902 2.9 61.3 1.0 C34 A:DJC902 3.3 71.8 1.0 C32 A:DJC902 3.4 63.7 1.0 CB A:ALA539 3.4 42.3 1.0 C38 A:DJC902 3.4 55.9 1.0 CA A:ALA539 4.0 45.5 1.0 C35 A:DJC902 4.0 73.4 1.0 C31 A:DJC902 4.0 63.3 1.0 C1 A:MPD901 4.1 77.5 1.0 O A:ALA539 4.2 64.3 1.0 C41 A:DJC902 4.3 62.2 1.0 C30 A:DJC902 4.3 68.7 1.0 C A:ALA539 4.6 56.6 1.0 C39 A:DJC902 4.6 58.0 1.0 C40 A:DJC902 4.9 67.3 1.0

Fluorine binding site 4 out of 4 in the LSD1-Fcpa-Mpe N5 Adduct Model


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of LSD1-Fcpa-Mpe N5 Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:74.3 occ:1.00 F3 A:DJC902 0.0 74.3 1.0 C42 A:DJC902 1.3 72.9 1.0 F1 A:DJC902 2.1 74.1 1.0 F2 A:DJC902 2.1 75.8 1.0 C37 A:DJC902 2.3 65.2 1.0 C38 A:DJC902 2.7 55.9 1.0 C1 A:MPD901 3.6 77.5 1.0 C36 A:DJC902 3.7 61.3 1.0 CE1 A:HIS564 3.7 64.7 1.0 C39 A:DJC902 4.0 58.0 1.0 C33 A:DJC902 4.3 64.4 1.0 CB A:ALA539 4.4 42.3 1.0 ND1 A:HIS564 4.4 64.6 1.0 C32 A:DJC902 4.7 63.7 1.0 C41 A:DJC902 4.7 62.2 1.0 NE2 A:HIS564 4.8 63.6 1.0 C40 A:DJC902 4.9 67.3 1.0 C2 A:MPD901 5.0 77.1 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