Fluorine in PDB 6kgq: LSD1-Fcpa-Mpe Five-Membered Ring Adduct Model

The structure of LSD1-Fcpa-Mpe Five-Membered Ring Adduct Model, PDB code: 6kgq 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 / 19.7

The binding sites of Fluorine atom in the LSD1-Fcpa-Mpe Five-Membered Ring Adduct Model (pdb code 6kgq). 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 Five-Membered Ring Adduct Model, PDB code: 6kgq:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the LSD1-Fcpa-Mpe 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-Fcpa-Mpe Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:76.7 occ:1.00 F A:DJC902 0.0 76.7 1.0 C40 A:DJC902 1.4 67.4 1.0 C39 A:DJC902 2.3 56.9 1.0 C41 A:DJC902 2.3 60.0 1.0 O A:HOH1143 2.6 51.8 1.0 O A:HOH1118 3.0 57.8 1.0 O A:HOH1051 3.3 52.5 1.0 C38 A:DJC902 3.6 56.9 1.0 C36 A:DJC902 3.6 60.6 1.0 O A:HOH1056 3.7 44.2 1.0 CG A:GLU559 3.8 91.1 1.0 C37 A:DJC902 4.1 65.5 1.0 OD2 A:ASP555 4.1 73.2 1.0 CD A:GLU559 4.6 96.1 1.0 CA A:GLU559 4.7 68.3 1.0 CB A:GLU559 4.7 76.4 1.0 OE2 A:GLU559 4.7 98.1 1.0 C33 A:DJC902 4.8 61.8 1.0 CG2 A:THR810 4.9 40.1 1.0 NE2 A:HIS812 5.0 40.8 1.0

Fluorine binding site 2 out of 4 in the LSD1-Fcpa-Mpe 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-Fcpa-Mpe Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:74.4 occ:1.00 F1 A:DJC902 0.0 74.4 1.0 C42 A:DJC902 1.3 72.8 1.0 F2 A:DJC902 2.1 74.4 1.0 F3 A:DJC902 2.1 76.4 1.0 C37 A:DJC902 2.3 65.5 1.0 C32 A:DJC902 3.0 64.3 1.0 C36 A:DJC902 3.1 60.6 1.0 C1 A:MPD901 3.1 76.8 1.0 C33 A:DJC902 3.2 61.8 1.0 C38 A:DJC902 3.4 56.9 1.0 CE1 A:HIS564 3.4 64.8 1.0 ND1 A:HIS564 3.6 64.6 1.0 C31 A:DJC902 3.9 59.4 1.0 C34 A:DJC902 4.3 65.1 1.0 C41 A:DJC902 4.4 60.0 1.0 C2 A:MPD901 4.4 77.2 1.0 NE2 A:HIS564 4.4 63.7 1.0 CG2 A:THR335 4.5 46.9 1.0 CM A:MPD901 4.5 73.3 1.0 C39 A:DJC902 4.6 56.9 1.0 O2 A:MPD901 4.8 79.0 1.0 CG A:HIS564 4.8 63.3 1.0 CG1 A:VAL333 4.8 44.7 1.0 C30 A:DJC902 4.9 57.4 1.0 C40 A:DJC902 4.9 67.4 1.0

Fluorine binding site 3 out of 4 in the LSD1-Fcpa-Mpe 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 3 of LSD1-Fcpa-Mpe Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:74.4 occ:1.00 F2 A:DJC902 0.0 74.4 1.0 C42 A:DJC902 1.3 72.8 1.0 F1 A:DJC902 2.1 74.4 1.0 F3 A:DJC902 2.1 76.4 1.0 C37 A:DJC902 2.3 65.5 1.0 C38 A:DJC902 2.6 56.9 1.0 C1 A:MPD901 3.6 76.8 1.0 C36 A:DJC902 3.7 60.6 1.0 CE1 A:HIS564 3.7 64.8 1.0 C39 A:DJC902 4.0 56.9 1.0 C33 A:DJC902 4.3 61.8 1.0 CB A:ALA539 4.4 41.6 1.0 ND1 A:HIS564 4.4 64.6 1.0 C32 A:DJC902 4.7 64.3 1.0 C41 A:DJC902 4.7 60.0 1.0 NE2 A:HIS564 4.8 63.7 1.0 C40 A:DJC902 4.8 67.4 1.0 C2 A:MPD901 5.0 77.2 1.0

Fluorine binding site 4 out of 4 in the LSD1-Fcpa-Mpe 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 4 of LSD1-Fcpa-Mpe Five-Membered Ring Adduct Model within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:76.4 occ:1.00 F3 A:DJC902 0.0 76.4 1.0 C42 A:DJC902 1.3 72.8 1.0 F2 A:DJC902 2.1 74.4 1.0 F1 A:DJC902 2.1 74.4 1.0 C37 A:DJC902 2.3 65.5 1.0 C36 A:DJC902 2.9 60.6 1.0 C33 A:DJC902 3.0 61.8 1.0 CB A:ALA539 3.3 41.6 1.0 C38 A:DJC902 3.4 56.9 1.0 C32 A:DJC902 3.5 64.3 1.0 C34 A:DJC902 3.5 65.1 1.0 CA A:ALA539 3.9 45.7 1.0 C1 A:MPD901 4.1 76.8 1.0 O A:ALA539 4.2 65.1 1.0 C31 A:DJC902 4.2 59.4 1.0 C41 A:DJC902 4.2 60.0 1.0 C35 A:DJC902 4.3 66.1 1.0 C A:ALA539 4.6 56.7 1.0 C30 A:DJC902 4.6 57.4 1.0 C39 A:DJC902 4.6 56.9 1.0 C40 A:DJC902 4.9 67.4 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