Bromine in PDB 7xe2: Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa

All present enzymatic activity of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa:
1.14.99.66;

The structure of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa, PDB code: 7xe2 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)	46.56 / 2.05
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	143.582, 170.082, 201.107, 90, 90, 90
R / Rfree (%)	16.7 / 19.4

The structure of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Bromine atom in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa (pdb code 7xe2). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa, PDB code: 7xe2:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Br905 b:62.7 occ:0.63 BR A:DIJ905 0.0 62.7 0.6 C2 A:DIJ905 1.9 38.3 0.6 C1 A:DIJ905 2.8 34.9 0.6 C3 A:DIJ905 2.8 26.5 0.6 CD1 A:ILE438 3.7 31.3 1.0 OH A:TYR698 3.7 37.1 1.0 OH A:TYR545 3.9 38.8 1.0 C A:DIJ905 4.1 35.5 0.6 C4 A:DIJ905 4.1 32.7 0.6 CZ A:TYR545 4.2 43.8 1.0 CE2 A:TYR545 4.5 39.0 1.0 C A:DIJ907 4.6 33.8 0.4 C5 A:DIJ905 4.7 31.5 0.6 C7 A:DIJ907 4.7 31.5 0.4 OD1 A:ASN440 4.8 48.7 1.0 CG2 A:ILE438 4.8 29.1 1.0 CE1 A:TYR545 4.8 33.7 1.0 O A:HOH1002 4.9 42.6 1.0 CZ A:TYR698 5.0 30.1 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa within 5.0Å range: probe atom residue distance (Å) B Occ A:Br907 b:66.9 occ:0.37 BR A:DIJ907 0.0 66.9 0.4 C2 A:DIJ907 1.9 38.3 0.4 C1 A:DIJ907 2.8 39.8 0.4 C3 A:DIJ907 2.8 33.9 0.4 O A:DIJ905 3.2 35.4 0.6 O A:HOH1302 3.2 45.8 1.0 CG2 A:THR804 3.5 24.4 1.0 ND2 A:ASN440 4.0 46.8 1.0 CG A:ASN440 4.1 44.0 1.0 CB A:ASN440 4.1 30.4 1.0 C A:DIJ907 4.1 33.8 0.4 C4 A:DIJ907 4.1 32.9 0.4 C8 A:DIJ905 4.2 33.0 0.6 O A:HOH1326 4.3 41.1 1.0 OE1 A:GLN803 4.6 30.4 1.0 O A:HOH1370 4.6 38.1 1.0 C5 A:DIJ907 4.7 31.9 0.4 OD1 A:ASN440 4.7 48.7 1.0 O A:HOH1333 4.8 54.3 1.0 C7 A:DIJ905 4.9 27.3 0.6 C4 A:DIJ905 5.0 32.7 0.6

Bromine binding site 3 out of 4 in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Br905 b:68.7 occ:0.60 BR B:DIJ905 0.0 68.7 0.6 C2 B:DIJ905 1.9 53.0 0.6 C3 B:DIJ905 2.8 44.2 0.6 C1 B:DIJ905 2.8 46.5 0.6 CD1 B:ILE438 3.7 46.7 1.0 OH B:TYR698 3.9 45.6 1.0 C4 B:DIJ905 4.1 43.1 0.6 C B:DIJ905 4.1 43.8 0.6 OH B:TYR545 4.2 53.9 1.0 CZ B:TYR545 4.4 54.3 1.0 CE2 B:TYR545 4.7 47.8 1.0 C5 B:DIJ905 4.7 43.0 0.6 C7 B:DIJ907 4.7 44.1 0.4 CG2 B:ILE438 4.7 40.6 1.0 ND2 B:ASN440 4.9 48.3 1.0 C B:DIJ907 4.9 43.2 0.4 OD1 B:ASN440 5.0 67.8 1.0 CG1 B:ILE438 5.0 43.7 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of LSD2 in Complex with Trans-4-Br-Pcpa within 5.0Å range: probe atom residue distance (Å) B Occ B:Br907 b:73.7 occ:0.41 BR B:DIJ907 0.0 73.7 0.4 C2 B:DIJ907 1.9 47.6 0.4 C1 B:DIJ907 2.8 47.2 0.4 C3 B:DIJ907 2.8 43.6 0.4 O B:DIJ905 3.2 45.4 0.6 CG2 B:THR804 3.6 33.8 1.0 ND2 B:ASN440 4.0 48.3 1.0 C B:DIJ907 4.1 43.2 0.4 C4 B:DIJ907 4.1 43.2 0.4 CB B:ASN440 4.2 42.5 1.0 CG B:ASN440 4.3 61.5 1.0 C8 B:DIJ905 4.3 40.2 0.6 O B:HOH1170 4.5 42.0 1.0 OE1 B:GLN803 4.6 39.6 1.0 C5 B:DIJ907 4.7 41.8 0.4 O B:HOH1307 4.7 42.2 1.0 C7 B:DIJ905 5.0 38.4 0.6 C4 B:DIJ905 5.0 43.1 0.6

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