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Fluorine in PDB 7xe3: Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)

Enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024)

All present enzymatic activity of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024):
1.14.99.66;

Protein crystallography data

The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024), PDB code: 7xe3 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) 48.27 / 2.82
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 143.372, 171.226, 201.918, 90, 90, 90
R / Rfree (%) 17.7 / 22.2

Other elements in 7xe3:

The structure of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) also contains other interesting chemical elements:

Bromine (Br) 2 atoms
Zinc (Zn) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) (pdb code 7xe3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024), PDB code: 7xe3:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7xe3

Go back to Fluorine Binding Sites List in 7xe3
Fluorine binding site 1 out of 4 in the Crystal Structure of LSD2 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 LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F905

b:49.1
occ:0.63
 F5 A:8A2905 0.0 49.1 0.6
C4 A:8A2905 1.3 44.5 0.6
C3 A:8A2905 2.3 46.2 0.6
C6 A:8A2905 2.3 45.4 0.6
C7 A:8A2905 2.8 46.7 0.6
CD2 A:TYR767 3.4 40.5 1.0
CE2 A:TYR767 3.4 40.2 1.0
CG A:TYR767 3.5 42.6 1.0
CZ A:TYR767 3.5 43.8 1.0
CB A:GLN803 3.5 43.3 1.0
C1 A:8A2905 3.6 48.8 0.6
C11 A:8A2905 3.6 48.7 0.6
CD1 A:TYR767 3.6 42.9 1.0
CE1 A:TYR767 3.6 46.4 1.0
OE1 A:GLN803 3.7 45.8 1.0
C12 A:8A2905 4.0 50.1 0.6
CD A:GLN803 4.1 45.9 1.0
O A:GLN803 4.1 43.0 1.0
OH A:TYR767 4.3 46.2 1.0
CB A:TYR767 4.3 44.5 1.0
C A:GLN803 4.3 42.2 1.0
CG A:GLN803 4.3 44.1 1.0
C8 A:8A2905 4.4 49.3 0.6
C10 A:FAD904 4.4 45.0 1.0
N10 A:FAD904 4.5 43.5 1.0
CA A:GLN803 4.5 40.9 1.0
N1 A:FAD904 4.6 45.2 1.0
CG2 A:THR804 4.7 40.2 1.0
C1' A:FAD904 4.7 40.4 1.0
C4X A:FAD904 4.8 44.1 1.0
NE2 A:GLN803 4.8 46.0 1.0
N A:THR804 4.9 40.4 1.0
N5 A:FAD904 4.9 45.6 1.0
O A:ALA546 5.0 51.7 1.0

Fluorine binding site 2 out of 4 in 7xe3

Go back to Fluorine Binding Sites List in 7xe3
Fluorine binding site 2 out of 4 in the Crystal Structure of LSD2 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 LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F905

b:46.0
occ:0.63
 F13 A:8A2905 0.0 46.0 0.6
C12 A:8A2905 1.4 50.1 0.6
C11 A:8A2905 2.4 48.7 0.6
C1 A:8A2905 2.4 48.8 0.6
CB A:ASN440 2.9 48.9 1.0
BR2 A:8A2905 3.1 58.6 0.6
O A:HOH1064 3.5 50.5 1.0
C3 A:8A2905 3.6 46.2 0.6
C6 A:8A2905 3.6 45.4 0.6
CA A:ASN440 4.0 47.7 1.0
C4 A:8A2905 4.0 44.5 0.6
N A:ASN440 4.1 40.3 1.0
CG2 A:ILE438 4.2 37.2 1.0
CG2 A:THR804 4.6 40.2 1.0
N3 A:FAD904 4.7 44.1 1.0
O A:ILE438 4.8 39.7 1.0
CB A:ILE438 4.8 37.7 1.0
C7 A:8A2905 4.9 46.7 0.6
C A:VAL439 4.9 40.8 1.0

Fluorine binding site 3 out of 4 in 7xe3

Go back to Fluorine Binding Sites List in 7xe3
Fluorine binding site 3 out of 4 in the Crystal Structure of LSD2 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 3 of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F905

b:51.8
occ:0.67
 F5 B:8A2905 0.0 51.8 0.7
C4 B:8A2905 1.3 54.5 0.7
C3 B:8A2905 2.3 56.8 0.7
C6 B:8A2905 2.3 60.5 0.7
C7 B:8A2905 2.8 59.8 0.7
CD2 B:TYR767 3.3 49.5 1.0
CE2 B:TYR767 3.3 46.1 1.0
CG B:TYR767 3.5 53.0 1.0
CZ B:TYR767 3.5 48.6 1.0
C1 B:8A2905 3.6 63.9 0.7
C11 B:8A2905 3.6 61.6 0.7
CB B:GLN803 3.7 39.4 1.0
CD1 B:TYR767 3.8 49.4 1.0
CE1 B:TYR767 3.8 50.4 1.0
OE1 B:GLN803 3.8 50.5 1.0
C12 B:8A2905 4.1 62.7 0.7
O B:GLN803 4.1 47.4 1.0
CD B:GLN803 4.2 45.7 1.0
OH B:TYR767 4.3 50.8 1.0
CB B:TYR767 4.3 49.3 1.0
C8 B:8A2905 4.4 62.2 0.7
C10 B:FAD904 4.4 57.2 1.0
C B:GLN803 4.4 42.6 1.0
CG B:GLN803 4.4 41.8 1.0
N10 B:FAD904 4.5 60.0 1.0
CA B:GLN803 4.6 41.0 1.0
N1 B:FAD904 4.7 53.2 1.0
C1' B:FAD904 4.7 50.1 1.0
C4X B:FAD904 4.8 57.8 1.0
N5 B:FAD904 4.9 60.3 1.0
O B:ALA546 4.9 47.5 1.0

Fluorine binding site 4 out of 4 in 7xe3

Go back to Fluorine Binding Sites List in 7xe3
Fluorine binding site 4 out of 4 in the Crystal Structure of LSD2 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 4 of Crystal Structure of LSD2 in Complex with Cis-4-Br-2,5-F2-Pcpa (S1024) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F905

b:59.0
occ:0.67
 F13 B:8A2905 0.0 59.0 0.7
C12 B:8A2905 1.4 62.7 0.7
C11 B:8A2905 2.4 61.6 0.7
C1 B:8A2905 2.4 63.9 0.7
CB B:ASN440 2.9 55.0 1.0
BR2 B:8A2905 3.1 71.6 0.7
C3 B:8A2905 3.6 56.8 0.7
C6 B:8A2905 3.6 60.5 0.7
CG2 B:ILE438 3.9 48.0 1.0
CA B:ASN440 4.0 55.4 1.0
C4 B:8A2905 4.1 54.5 0.7
N B:ASN440 4.1 53.1 1.0
CB B:ILE438 4.8 50.7 1.0
C7 B:8A2905 4.9 59.8 0.7
N3 B:FAD904 4.9 57.7 1.0
C B:VAL439 5.0 52.9 1.0

Reference:

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
Page generated: Wed Jul 16 01:53:12 2025

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