Fluorine in PDB 4e28: Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Enzymatic activity of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
All present enzymatic activity of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor:
2.1.1.45;
Protein crystallography data
The structure of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor, PDB code: 4e28
was solved by
A.Tochowicz,
J.Finer-Moore,
R.M.Stroud,
M.P.Costi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.23 /
2.30
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.747,
95.747,
82.407,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.8 /
22.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
(pdb code 4e28). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor, PDB code: 4e28:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 1 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:0.7
occ:0.32
|
F28
|
A:0MZ403
|
0.0
|
0.7
|
0.3
|
H24
|
A:9MZ404
|
1.2
|
1.0
|
0.7
|
C27
|
A:0MZ403
|
1.3
|
0.7
|
0.3
|
C24
|
A:9MZ404
|
1.6
|
0.9
|
0.7
|
F29
|
A:9MZ404
|
1.9
|
1.0
|
0.7
|
C25
|
A:9MZ404
|
2.0
|
0.5
|
0.7
|
F30
|
A:0MZ403
|
2.2
|
0.2
|
0.3
|
F29
|
A:0MZ403
|
2.2
|
0.1
|
0.3
|
C27
|
A:9MZ404
|
2.3
|
0.6
|
0.7
|
C25
|
A:0MZ403
|
2.3
|
0.1
|
0.3
|
H26
|
A:0MZ403
|
2.3
|
0.4
|
0.3
|
C26
|
A:0MZ403
|
2.7
|
0.6
|
0.3
|
C23
|
A:9MZ404
|
2.7
|
0.3
|
0.7
|
F30
|
A:9MZ404
|
2.8
|
0.8
|
0.7
|
H23
|
A:9MZ404
|
3.2
|
0.1
|
0.7
|
C26
|
A:9MZ404
|
3.3
|
0.6
|
0.7
|
F28
|
A:9MZ404
|
3.5
|
0.1
|
0.7
|
C24
|
A:0MZ403
|
3.6
|
0.5
|
0.3
|
C22
|
A:9MZ404
|
3.8
|
1.0
|
0.7
|
H24
|
A:0MZ403
|
4.0
|
0.5
|
0.3
|
C21
|
A:9MZ404
|
4.0
|
0.7
|
0.7
|
C21
|
A:0MZ403
|
4.0
|
0.9
|
0.3
|
H26
|
A:9MZ404
|
4.1
|
0.3
|
0.7
|
C23
|
A:0MZ403
|
4.7
|
0.4
|
0.3
|
H22
|
A:9MZ404
|
4.7
|
0.5
|
0.7
|
N18
|
A:0MZ403
|
4.9
|
0.5
|
0.3
|
C22
|
A:0MZ403
|
4.9
|
0.2
|
0.3
|
|
Fluorine binding site 2 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 2 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:0.2
occ:0.32
|
F30
|
A:0MZ403
|
0.0
|
0.2
|
0.3
|
F29
|
A:9MZ404
|
0.9
|
1.0
|
0.7
|
C27
|
A:0MZ403
|
1.3
|
0.7
|
0.3
|
C27
|
A:9MZ404
|
1.4
|
0.6
|
0.7
|
F30
|
A:9MZ404
|
1.5
|
0.8
|
0.7
|
F28
|
A:0MZ403
|
2.2
|
0.7
|
0.3
|
F29
|
A:0MZ403
|
2.2
|
0.1
|
0.3
|
C25
|
A:0MZ403
|
2.3
|
0.1
|
0.3
|
F28
|
A:9MZ404
|
2.3
|
0.1
|
0.7
|
C25
|
A:9MZ404
|
2.6
|
0.5
|
0.7
|
H24
|
A:9MZ404
|
2.8
|
1.0
|
0.7
|
C24
|
A:0MZ403
|
3.0
|
0.5
|
0.3
|
H24
|
A:0MZ403
|
3.1
|
0.5
|
0.3
|
C24
|
A:9MZ404
|
3.1
|
0.9
|
0.7
|
C26
|
A:0MZ403
|
3.2
|
0.6
|
0.3
|
H26
|
A:0MZ403
|
3.4
|
0.4
|
0.3
|
O
|
A:LEU101
|
3.6
|
0.1
|
1.0
|
C26
|
A:9MZ404
|
3.8
|
0.6
|
0.7
|
H26
|
A:9MZ404
|
4.0
|
0.3
|
0.7
|
C23
|
A:0MZ403
|
4.3
|
0.4
|
0.3
|
C23
|
A:9MZ404
|
4.4
|
0.3
|
0.7
|
C21
|
A:0MZ403
|
4.4
|
0.9
|
0.3
|
C
|
A:LEU101
|
4.8
|
0.9
|
1.0
|
C22
|
A:0MZ403
|
4.9
|
0.2
|
0.3
|
C21
|
A:9MZ404
|
5.0
|
0.7
|
0.7
|
|
Fluorine binding site 3 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 3 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:0.1
occ:0.32
|
F29
|
A:0MZ403
|
0.0
|
0.1
|
0.3
|
C27
|
A:0MZ403
|
1.3
|
0.7
|
0.3
|
H24
|
A:9MZ404
|
1.7
|
1.0
|
0.7
|
F30
|
A:9MZ404
|
1.9
|
0.8
|
0.7
|
F30
|
A:0MZ403
|
2.2
|
0.2
|
0.3
|
F28
|
A:0MZ403
|
2.2
|
0.7
|
0.3
|
C25
|
A:0MZ403
|
2.3
|
0.1
|
0.3
|
C24
|
A:9MZ404
|
2.4
|
0.9
|
0.7
|
H24
|
A:0MZ403
|
2.6
|
0.5
|
0.3
|
C27
|
A:9MZ404
|
2.6
|
0.6
|
0.7
|
F29
|
A:9MZ404
|
2.8
|
1.0
|
0.7
|
C24
|
A:0MZ403
|
2.8
|
0.5
|
0.3
|
C25
|
A:9MZ404
|
2.8
|
0.5
|
0.7
|
C26
|
A:0MZ403
|
3.5
|
0.6
|
0.3
|
C23
|
A:9MZ404
|
3.6
|
0.3
|
0.7
|
H26
|
A:0MZ403
|
3.8
|
0.4
|
0.3
|
F28
|
A:9MZ404
|
3.8
|
0.1
|
0.7
|
H23
|
A:9MZ404
|
4.0
|
0.1
|
0.7
|
C23
|
A:0MZ403
|
4.1
|
0.4
|
0.3
|
C26
|
A:9MZ404
|
4.2
|
0.6
|
0.7
|
C21
|
A:0MZ403
|
4.6
|
0.9
|
0.3
|
C22
|
A:9MZ404
|
4.8
|
1.0
|
0.7
|
H23
|
A:0MZ403
|
4.8
|
0.0
|
0.3
|
H26
|
A:9MZ404
|
4.8
|
0.3
|
0.7
|
C22
|
A:0MZ403
|
4.9
|
0.2
|
0.3
|
C21
|
A:9MZ404
|
5.0
|
0.7
|
0.7
|
|
Fluorine binding site 4 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 4 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:0.1
occ:0.68
|
F28
|
A:9MZ404
|
0.0
|
0.1
|
0.7
|
C27
|
A:9MZ404
|
1.3
|
0.6
|
0.7
|
F29
|
A:9MZ404
|
2.1
|
1.0
|
0.7
|
F30
|
A:9MZ404
|
2.2
|
0.8
|
0.7
|
C25
|
A:0MZ403
|
2.2
|
0.1
|
0.3
|
H26
|
A:9MZ404
|
2.3
|
0.3
|
0.7
|
C25
|
A:9MZ404
|
2.3
|
0.5
|
0.7
|
F30
|
A:0MZ403
|
2.3
|
0.2
|
0.3
|
C26
|
A:0MZ403
|
2.5
|
0.6
|
0.3
|
C24
|
A:0MZ403
|
2.6
|
0.5
|
0.3
|
C26
|
A:9MZ404
|
2.6
|
0.6
|
0.7
|
C27
|
A:0MZ403
|
2.7
|
0.7
|
0.3
|
H26
|
A:0MZ403
|
3.0
|
0.4
|
0.3
|
O
|
A:LEU101
|
3.1
|
0.1
|
1.0
|
H24
|
A:0MZ403
|
3.1
|
0.5
|
0.3
|
C21
|
A:0MZ403
|
3.1
|
0.9
|
0.3
|
C23
|
A:0MZ403
|
3.2
|
0.4
|
0.3
|
C22
|
A:0MZ403
|
3.4
|
0.2
|
0.3
|
F28
|
A:0MZ403
|
3.5
|
0.7
|
0.3
|
C24
|
A:9MZ404
|
3.6
|
0.9
|
0.7
|
F29
|
A:0MZ403
|
3.8
|
0.1
|
0.3
|
CG
|
A:LEU101
|
3.8
|
98.2
|
1.0
|
H24
|
A:9MZ404
|
4.0
|
1.0
|
0.7
|
H23
|
A:0MZ403
|
4.0
|
0.0
|
0.3
|
C21
|
A:9MZ404
|
4.0
|
0.7
|
0.7
|
CD2
|
A:LEU101
|
4.0
|
95.0
|
1.0
|
O19
|
A:9MZ404
|
4.1
|
0.8
|
0.7
|
N18
|
A:0MZ403
|
4.1
|
0.5
|
0.3
|
C
|
A:LEU101
|
4.3
|
0.9
|
1.0
|
H22
|
A:0MZ403
|
4.3
|
0.5
|
0.3
|
CB
|
A:LEU101
|
4.5
|
0.7
|
1.0
|
C23
|
A:9MZ404
|
4.7
|
0.3
|
0.7
|
C22
|
A:9MZ404
|
4.9
|
1.0
|
0.7
|
C17
|
A:9MZ404
|
4.9
|
0.7
|
0.7
|
N18
|
A:9MZ404
|
4.9
|
0.3
|
0.7
|
CD1
|
A:LEU101
|
4.9
|
94.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 5 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:0.8
occ:0.68
|
F30
|
A:9MZ404
|
0.0
|
0.8
|
0.7
|
C27
|
A:9MZ404
|
1.3
|
0.6
|
0.7
|
C27
|
A:0MZ403
|
1.5
|
0.7
|
0.3
|
F30
|
A:0MZ403
|
1.5
|
0.2
|
0.3
|
H24
|
A:0MZ403
|
1.5
|
0.5
|
0.3
|
C25
|
A:0MZ403
|
1.6
|
0.1
|
0.3
|
C24
|
A:0MZ403
|
1.6
|
0.5
|
0.3
|
F29
|
A:0MZ403
|
1.9
|
0.1
|
0.3
|
F28
|
A:9MZ404
|
2.2
|
0.1
|
0.7
|
F29
|
A:9MZ404
|
2.2
|
1.0
|
0.7
|
C25
|
A:9MZ404
|
2.3
|
0.5
|
0.7
|
F28
|
A:0MZ403
|
2.8
|
0.7
|
0.3
|
H24
|
A:9MZ404
|
2.8
|
1.0
|
0.7
|
C26
|
A:0MZ403
|
2.9
|
0.6
|
0.3
|
C24
|
A:9MZ404
|
2.9
|
0.9
|
0.7
|
C23
|
A:0MZ403
|
3.0
|
0.4
|
0.3
|
C26
|
A:9MZ404
|
3.4
|
0.6
|
0.7
|
H26
|
A:0MZ403
|
3.5
|
0.4
|
0.3
|
H26
|
A:9MZ404
|
3.6
|
0.3
|
0.7
|
H23
|
A:0MZ403
|
3.6
|
0.0
|
0.3
|
O
|
A:LEU101
|
3.6
|
0.1
|
1.0
|
C21
|
A:0MZ403
|
3.8
|
0.9
|
0.3
|
C22
|
A:0MZ403
|
3.8
|
0.2
|
0.3
|
C23
|
A:9MZ404
|
4.2
|
0.3
|
0.7
|
C21
|
A:9MZ404
|
4.5
|
0.7
|
0.7
|
CA
|
A:SER102
|
4.8
|
0.3
|
1.0
|
C
|
A:LEU101
|
4.8
|
0.9
|
1.0
|
H22
|
A:0MZ403
|
4.8
|
0.5
|
0.3
|
C22
|
A:9MZ404
|
4.9
|
1.0
|
0.7
|
H23
|
A:9MZ404
|
5.0
|
0.1
|
0.7
|
|
Fluorine binding site 6 out
of 6 in 4e28
Go back to
Fluorine Binding Sites List in 4e28
Fluorine binding site 6 out
of 6 in the Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Structure of Human Thymidylate Synthase in Inactive Conformation with A Novel Non-Peptidic Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:1.0
occ:0.68
|
F29
|
A:9MZ404
|
0.0
|
1.0
|
0.7
|
F30
|
A:0MZ403
|
0.9
|
0.2
|
0.3
|
C27
|
A:9MZ404
|
1.3
|
0.6
|
0.7
|
C27
|
A:0MZ403
|
1.6
|
0.7
|
0.3
|
F28
|
A:0MZ403
|
1.9
|
0.7
|
0.3
|
F28
|
A:9MZ404
|
2.1
|
0.1
|
0.7
|
F30
|
A:9MZ404
|
2.2
|
0.8
|
0.7
|
C25
|
A:9MZ404
|
2.3
|
0.5
|
0.7
|
C25
|
A:0MZ403
|
2.4
|
0.1
|
0.3
|
F29
|
A:0MZ403
|
2.8
|
0.1
|
0.3
|
H24
|
A:9MZ404
|
2.8
|
1.0
|
0.7
|
H26
|
A:0MZ403
|
2.8
|
0.4
|
0.3
|
C24
|
A:9MZ404
|
2.9
|
0.9
|
0.7
|
C26
|
A:0MZ403
|
2.9
|
0.6
|
0.3
|
C26
|
A:9MZ404
|
3.4
|
0.6
|
0.7
|
C24
|
A:0MZ403
|
3.4
|
0.5
|
0.3
|
H26
|
A:9MZ404
|
3.6
|
0.3
|
0.7
|
H24
|
A:0MZ403
|
3.7
|
0.5
|
0.3
|
O
|
A:LEU101
|
3.9
|
0.1
|
1.0
|
C21
|
A:0MZ403
|
4.2
|
0.9
|
0.3
|
C23
|
A:9MZ404
|
4.2
|
0.3
|
0.7
|
C23
|
A:0MZ403
|
4.5
|
0.4
|
0.3
|
C21
|
A:9MZ404
|
4.6
|
0.7
|
0.7
|
C22
|
A:0MZ403
|
4.8
|
0.2
|
0.3
|
C22
|
A:9MZ404
|
4.9
|
1.0
|
0.7
|
H23
|
A:9MZ404
|
4.9
|
0.1
|
0.7
|
|
Reference:
E.Carosati,
A.Tochowicz,
G.Marverti,
G.Guaitoli,
P.Benedetti,
S.Ferrari,
R.M.Stroud,
J.Finer-Moore,
R.Luciani,
D.Farina,
G.Cruciani,
M.P.Costi.
Inhibitor of Ovarian Cancer Cells Growth By Virtual Screening: A New Thiazole Derivative Targeting Human Thymidylate Synthase. J.Med.Chem. V. 55 10272 2012.
ISSN: ISSN 0022-2623
PubMed: 23075414
DOI: 10.1021/JM300850V
Page generated: Thu Aug 1 01:10:14 2024
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