Fluorine in PDB 5b1s: Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
Enzymatic activity of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
All present enzymatic activity of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine:
2.5.1.16;
Protein crystallography data
The structure of Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine, PDB code: 5b1s
was solved by
Y.Amano,
Y.Tateishi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.02 /
1.58
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.484,
68.163,
94.458,
87.91,
87.18,
80.27
|
R / Rfree (%)
|
18.5 /
23.2
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
(pdb code 5b1s). 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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine, PDB code: 5b1s:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 5b1s
Go back to
Fluorine Binding Sites List in 5b1s
Fluorine binding site 1 out
of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:16.0
occ:1.00
|
F10
|
A:BSX502
|
0.0
|
16.0
|
1.0
|
C3
|
A:BSX502
|
1.4
|
14.0
|
1.0
|
C6
|
A:BSX502
|
2.4
|
14.4
|
1.0
|
C1
|
A:BSX502
|
2.4
|
12.9
|
1.0
|
O
|
A:HOH626
|
2.9
|
12.9
|
1.0
|
C2
|
A:BSX502
|
2.9
|
13.9
|
1.0
|
CA
|
A:THR170
|
3.2
|
12.2
|
1.0
|
C5
|
A:BSX502
|
3.4
|
15.4
|
1.0
|
NE2
|
A:GLN64
|
3.4
|
12.0
|
1.0
|
N
|
A:ASP171
|
3.4
|
11.6
|
1.0
|
O
|
A:THR169
|
3.5
|
12.4
|
1.0
|
C4
|
A:BSX502
|
3.6
|
12.6
|
1.0
|
C
|
A:THR170
|
3.6
|
11.5
|
1.0
|
C9
|
A:BSX502
|
3.6
|
12.7
|
1.0
|
OE1
|
A:GLN64
|
3.7
|
14.0
|
1.0
|
OD2
|
A:ASP171
|
3.8
|
12.6
|
1.0
|
CD
|
A:GLN64
|
3.9
|
12.5
|
1.0
|
OE1
|
A:GLN201
|
3.9
|
15.4
|
1.0
|
C7
|
A:BSX502
|
4.1
|
11.0
|
1.0
|
CG
|
A:ASP171
|
4.1
|
12.9
|
1.0
|
N
|
A:THR170
|
4.2
|
10.5
|
1.0
|
CB
|
A:THR170
|
4.2
|
10.7
|
1.0
|
C
|
A:THR169
|
4.2
|
11.4
|
1.0
|
N8
|
A:BSX502
|
4.3
|
12.7
|
1.0
|
CG2
|
A:THR170
|
4.4
|
12.2
|
1.0
|
CA
|
A:ASP171
|
4.5
|
11.7
|
1.0
|
OD1
|
A:ASP171
|
4.5
|
12.4
|
1.0
|
O
|
A:THR170
|
4.5
|
13.0
|
1.0
|
CD
|
A:GLN201
|
4.6
|
10.4
|
1.0
|
CB
|
A:ASP171
|
4.8
|
11.7
|
1.0
|
CG
|
A:GLN201
|
4.8
|
10.8
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 5b1s
Go back to
Fluorine Binding Sites List in 5b1s
Fluorine binding site 2 out
of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:17.9
occ:1.00
|
F10
|
B:BSX502
|
0.0
|
17.9
|
1.0
|
C3
|
B:BSX502
|
1.3
|
15.5
|
1.0
|
C6
|
B:BSX502
|
2.2
|
14.5
|
1.0
|
C1
|
B:BSX502
|
2.4
|
14.4
|
1.0
|
O
|
B:HOH660
|
2.9
|
14.1
|
1.0
|
C2
|
B:BSX502
|
3.0
|
14.4
|
1.0
|
CA
|
B:THR170
|
3.3
|
12.9
|
1.0
|
C5
|
B:BSX502
|
3.3
|
15.8
|
1.0
|
NE2
|
B:GLN64
|
3.5
|
12.5
|
1.0
|
O
|
B:THR169
|
3.5
|
13.7
|
1.0
|
N
|
B:ASP171
|
3.5
|
12.0
|
1.0
|
C9
|
B:BSX502
|
3.5
|
13.9
|
1.0
|
C4
|
B:BSX502
|
3.6
|
14.6
|
1.0
|
C
|
B:THR170
|
3.6
|
12.4
|
1.0
|
OE1
|
B:GLN64
|
3.7
|
13.5
|
1.0
|
OD2
|
B:ASP171
|
3.9
|
12.7
|
1.0
|
C7
|
B:BSX502
|
3.9
|
12.7
|
1.0
|
CD
|
B:GLN64
|
3.9
|
13.5
|
1.0
|
NE2
|
B:GLN201
|
4.0
|
11.0
|
1.0
|
N
|
B:THR170
|
4.2
|
11.3
|
1.0
|
C
|
B:THR169
|
4.2
|
12.3
|
1.0
|
CG
|
B:ASP171
|
4.2
|
12.3
|
1.0
|
CB
|
B:THR170
|
4.2
|
12.9
|
1.0
|
N8
|
B:BSX502
|
4.3
|
12.9
|
1.0
|
CG2
|
B:THR170
|
4.5
|
12.0
|
1.0
|
O
|
B:THR170
|
4.5
|
13.0
|
1.0
|
CA
|
B:ASP171
|
4.5
|
13.3
|
1.0
|
CD
|
B:GLN201
|
4.6
|
9.8
|
1.0
|
OD1
|
B:ASP171
|
4.6
|
14.8
|
1.0
|
CG
|
B:GLN201
|
4.8
|
10.2
|
1.0
|
CB
|
B:ASP171
|
4.9
|
11.7
|
1.0
|
CG
|
B:S4M501
|
5.0
|
18.9
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 5b1s
Go back to
Fluorine Binding Sites List in 5b1s
Fluorine binding site 3 out
of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:20.0
occ:1.00
|
F10
|
C:BSX502
|
0.0
|
20.0
|
1.0
|
C3
|
C:BSX502
|
1.4
|
16.0
|
1.0
|
C6
|
C:BSX502
|
2.3
|
15.9
|
1.0
|
C1
|
C:BSX502
|
2.4
|
16.1
|
1.0
|
O
|
C:HOH625
|
2.9
|
15.8
|
1.0
|
C2
|
C:BSX502
|
3.0
|
16.3
|
1.0
|
CA
|
C:THR170
|
3.3
|
12.8
|
1.0
|
C5
|
C:BSX502
|
3.3
|
16.4
|
1.0
|
NE2
|
C:GLN64
|
3.5
|
14.1
|
1.0
|
N
|
C:ASP171
|
3.5
|
11.6
|
1.0
|
O
|
C:THR169
|
3.5
|
13.3
|
1.0
|
C
|
C:THR170
|
3.6
|
12.8
|
1.0
|
C4
|
C:BSX502
|
3.6
|
16.4
|
1.0
|
OE1
|
C:GLN64
|
3.6
|
14.3
|
1.0
|
C9
|
C:BSX502
|
3.6
|
16.4
|
1.0
|
OD2
|
C:ASP171
|
3.8
|
12.4
|
1.0
|
CD
|
C:GLN64
|
3.9
|
15.3
|
1.0
|
OE1
|
C:GLN201
|
3.9
|
14.4
|
1.0
|
C7
|
C:BSX502
|
4.1
|
14.3
|
1.0
|
N
|
C:THR170
|
4.1
|
13.2
|
1.0
|
C
|
C:THR169
|
4.2
|
13.8
|
1.0
|
CG
|
C:ASP171
|
4.2
|
12.7
|
1.0
|
CB
|
C:THR170
|
4.2
|
12.9
|
1.0
|
N8
|
C:BSX502
|
4.3
|
11.2
|
1.0
|
CG2
|
C:THR170
|
4.3
|
14.6
|
1.0
|
O
|
C:THR170
|
4.5
|
14.5
|
1.0
|
CD
|
C:GLN201
|
4.5
|
11.1
|
1.0
|
CA
|
C:ASP171
|
4.6
|
12.2
|
1.0
|
OD1
|
C:ASP171
|
4.6
|
14.9
|
1.0
|
CG
|
C:GLN201
|
4.7
|
10.5
|
1.0
|
CB
|
C:ASP171
|
4.9
|
13.8
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 5b1s
Go back to
Fluorine Binding Sites List in 5b1s
Fluorine binding site 4 out
of 4 in the Crystal Structure of Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine
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 Trypanosoma Cruzi Spermidine Synthase in Complex with 2-(2-Fluorophenyl)Ethanamine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F502
b:17.4
occ:1.00
|
F10
|
D:BSX502
|
0.0
|
17.4
|
1.0
|
C3
|
D:BSX502
|
1.4
|
15.9
|
1.0
|
C6
|
D:BSX502
|
2.3
|
15.1
|
1.0
|
C1
|
D:BSX502
|
2.4
|
14.8
|
1.0
|
C2
|
D:BSX502
|
2.8
|
12.7
|
1.0
|
O
|
D:HOH637
|
3.0
|
12.2
|
1.0
|
CA
|
D:THR170
|
3.2
|
10.9
|
1.0
|
C5
|
D:BSX502
|
3.3
|
12.9
|
1.0
|
NE2
|
D:GLN64
|
3.4
|
12.1
|
1.0
|
N
|
D:ASP171
|
3.5
|
11.3
|
1.0
|
O
|
D:THR169
|
3.5
|
13.0
|
1.0
|
C4
|
D:BSX502
|
3.6
|
13.7
|
1.0
|
C9
|
D:BSX502
|
3.6
|
16.6
|
1.0
|
C
|
D:THR170
|
3.6
|
11.3
|
1.0
|
OE1
|
D:GLN64
|
3.6
|
12.0
|
1.0
|
OD2
|
D:ASP171
|
3.8
|
13.0
|
1.0
|
NE2
|
D:GLN201
|
3.9
|
10.7
|
1.0
|
CD
|
D:GLN64
|
3.9
|
12.2
|
1.0
|
C7
|
D:BSX502
|
4.1
|
14.0
|
1.0
|
CG
|
D:ASP171
|
4.1
|
11.8
|
1.0
|
N
|
D:THR170
|
4.1
|
11.2
|
1.0
|
CB
|
D:THR170
|
4.2
|
10.5
|
1.0
|
C
|
D:THR169
|
4.2
|
10.9
|
1.0
|
N8
|
D:BSX502
|
4.3
|
11.9
|
1.0
|
CA
|
D:ASP171
|
4.5
|
12.5
|
1.0
|
O
|
D:THR170
|
4.5
|
12.1
|
1.0
|
CG2
|
D:THR170
|
4.5
|
11.8
|
1.0
|
CD
|
D:GLN201
|
4.6
|
10.5
|
1.0
|
OD1
|
D:ASP171
|
4.6
|
13.5
|
1.0
|
CB
|
D:ASP171
|
4.8
|
11.6
|
1.0
|
CG
|
D:GLN201
|
4.8
|
9.5
|
1.0
|
O
|
D:ILE63
|
5.0
|
12.0
|
1.0
|
CG
|
D:S4M501
|
5.0
|
17.6
|
1.0
|
|
Reference:
R.Yoshino,
N.Yasuo,
Y.Hagiwara,
T.Ishida,
D.K.Inaoka,
Y.Amano,
Y.Tateishi,
K.Ohno,
I.Namatame,
T.Niimi,
M.Orita,
K.Kita,
Y.Akiyama,
M.Sekijima.
In Silico, in Vitro, X-Ray Crystallography, and Integrated Strategies For Discovering Spermidine Synthase Inhibitors For Chagas Disease Sci Rep V. 7 6666 2017.
ISSN: ESSN 2045-2322
PubMed: 28751689
DOI: 10.1038/S41598-017-06411-9
Page generated: Thu Aug 1 08:01:28 2024
|