Fluorine in PDB 7w3l: Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)

All present enzymatic activity of Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024):
1.14.99.66;

The structure of Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024), PDB code: 7w3l 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)	48.12 / 2.51
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	186.433, 186.433, 107.457, 90, 90, 120
R / Rfree (%)	17.8 / 21.6

The structure of Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) also contains other interesting chemical elements:

Bromine

(Br)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) (pdb code 7w3l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024), PDB code: 7w3l:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:62.7 occ:1.00 F5 A:8A2902 0.0 62.7 1.0 C4 A:8A2902 1.3 58.9 1.0 C3 A:8A2902 2.3 64.6 1.0 C6 A:8A2902 2.4 59.6 1.0 C8 A:8A2902 2.8 50.2 1.0 C7 A:8A2902 2.9 59.2 1.0 O4 A:FAD901 3.1 61.7 1.0 C4 A:FAD901 3.2 54.9 1.0 N3 A:FAD901 3.4 48.7 1.0 C1 A:8A2902 3.6 73.9 1.0 C11 A:8A2902 3.6 53.0 1.0 C4X A:FAD901 4.0 50.9 1.0 C9 A:8A2902 4.0 52.4 1.0 CB A:VAL333 4.0 59.4 1.0 O A:HOH1109 4.0 66.6 1.0 O A:HOH1123 4.1 67.8 1.0 C12 A:8A2902 4.1 64.7 1.0 C2 A:FAD901 4.2 48.7 1.0 CG1 A:VAL333 4.2 60.2 1.0 N5 A:FAD901 4.4 52.6 1.0 O A:HOH1120 4.5 80.7 1.0 O10 A:8A2902 4.5 61.3 1.0 CG2 A:VAL333 4.7 60.1 1.0 C10 A:FAD901 4.7 41.9 1.0 O A:VAL333 4.7 51.9 1.0 N1 A:FAD901 4.8 48.7 1.0 CG2 A:THR335 4.8 52.2 1.0 O2 A:FAD901 4.9 50.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of LSD1 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:73.8 occ:1.00 F13 A:8A2902 0.0 73.8 1.0 C12 A:8A2902 1.3 64.7 1.0 C11 A:8A2902 2.3 53.0 1.0 C1 A:8A2902 2.4 73.9 1.0 C1 A:GOL909 3.1 72.1 1.0 BR2 A:8A2902 3.1 112.4 1.0 O1 A:GOL909 3.2 69.9 1.0 CB A:ALA809 3.5 44.7 1.0 CG2 A:THR810 3.5 43.6 1.0 O A:PRO808 3.6 52.6 1.0 C6 A:8A2902 3.6 59.6 1.0 O A:ALA809 3.6 55.9 1.0 C3 A:8A2902 3.6 64.6 1.0 C2 A:GOL909 3.9 72.5 1.0 C A:ALA809 4.0 48.2 1.0 O A:HOH1042 4.0 55.6 1.0 C4 A:8A2902 4.1 58.9 1.0 CA A:ALA809 4.3 46.1 1.0 C3 A:GOL909 4.5 80.6 1.0 O A:ALA539 4.6 52.0 1.0 C A:PRO808 4.6 54.5 1.0 N A:THR810 4.7 51.3 1.0 C7 A:8A2902 4.7 59.2 1.0 CE2 A:TYR761 4.9 48.2 1.0 CB A:THR810 4.9 50.3 1.0 N A:ALA809 4.9 48.8 1.0 CD2 A:TYR761 5.0 48.9 1.0 OD2 A:ASP555 5.0 65.0 1.0

H.Niwa, C.Watanabe, S.Sato, T.Harada, H.Watanabe, R.Tabusa, S.Fukasawa, A.Shiobara, T.Hashimoto, O.Ohno, K.Nakamura, K.Tsuganezawa, A.Tanaka, M.Shirouzu, T.Honma, K.Matsuno, T.Umehara. Structure-Activity Relationship and in Silico Evaluation of Cis- and Trans-Pcpa-Derived Inhibitors of LSD1 and LSD2 Acs Med.Chem.Lett. V. 13 1485 2022.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.2C00294