Fluorine in PDB 6zxo: Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
Enzymatic activity of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
All present enzymatic activity of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex):
2.1.1.45;
Protein crystallography data
The structure of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex), PDB code: 6zxo
was solved by
C.Pozzi,
S.Mangani,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.33 /
2.60
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
61.72,
95.87,
103.84,
112.39,
91.47,
109.17
|
R / Rfree (%)
|
17.2 /
23.2
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
(pdb code 6zxo). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex), PDB code: 6zxo:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6zxo
Go back to
Fluorine Binding Sites List in 6zxo
Fluorine binding site 1 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F402
b:61.4
occ:1.00
|
F5
|
A:UFP402
|
0.0
|
61.4
|
1.0
|
C5
|
A:UFP402
|
1.4
|
49.4
|
1.0
|
C6
|
A:UFP402
|
2.4
|
47.7
|
1.0
|
C4
|
A:UFP402
|
2.4
|
47.2
|
1.0
|
O4
|
A:UFP402
|
2.8
|
50.0
|
1.0
|
CH2
|
A:TRP109
|
3.4
|
45.1
|
1.0
|
C6
|
A:D16401
|
3.6
|
48.1
|
1.0
|
N3
|
A:UFP402
|
3.6
|
41.6
|
1.0
|
N1
|
A:UFP402
|
3.6
|
39.5
|
1.0
|
CZ2
|
A:TRP109
|
3.7
|
43.4
|
1.0
|
C7
|
A:D16401
|
3.8
|
49.4
|
1.0
|
C9
|
A:D16401
|
3.8
|
49.2
|
1.0
|
C5
|
A:D16401
|
3.9
|
42.1
|
1.0
|
C2
|
A:UFP402
|
4.1
|
39.4
|
1.0
|
CD2
|
A:LEU192
|
4.1
|
73.9
|
1.0
|
SG
|
A:CYS195
|
4.2
|
81.3
|
1.0
|
CP1
|
A:D16401
|
4.2
|
57.3
|
1.0
|
C8
|
A:D16401
|
4.3
|
45.1
|
1.0
|
C4A
|
A:D16401
|
4.5
|
40.7
|
1.0
|
N10
|
A:D16401
|
4.5
|
55.2
|
1.0
|
OH
|
A:TYR135
|
4.6
|
62.4
|
1.0
|
CZ3
|
A:TRP109
|
4.6
|
46.3
|
1.0
|
C8A
|
A:D16401
|
4.7
|
41.2
|
1.0
|
CB
|
A:CYS195
|
4.8
|
67.2
|
1.0
|
C1'
|
A:UFP402
|
4.9
|
35.1
|
1.0
|
O4'
|
A:UFP402
|
4.9
|
37.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6zxo
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Fluorine Binding Sites List in 6zxo
Fluorine binding site 2 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F402
b:77.5
occ:1.00
|
F5
|
B:UFP402
|
0.0
|
77.5
|
1.0
|
C5
|
B:UFP402
|
1.3
|
52.6
|
1.0
|
C6
|
B:UFP402
|
2.3
|
47.7
|
1.0
|
C4
|
B:UFP402
|
2.4
|
51.0
|
1.0
|
O4
|
B:UFP402
|
2.8
|
51.7
|
1.0
|
N1
|
B:UFP402
|
3.5
|
45.0
|
1.0
|
N3
|
B:UFP402
|
3.6
|
48.8
|
1.0
|
CH2
|
B:TRP109
|
3.7
|
57.0
|
1.0
|
SG
|
B:CYS195
|
3.7
|
94.2
|
1.0
|
C6
|
B:D16401
|
3.8
|
46.3
|
1.0
|
CZ2
|
B:TRP109
|
4.0
|
52.2
|
1.0
|
CD2
|
B:LEU192
|
4.0
|
57.3
|
1.0
|
C9
|
B:D16401
|
4.0
|
53.0
|
1.0
|
CP1
|
B:D16401
|
4.0
|
62.8
|
1.0
|
C7
|
B:D16401
|
4.0
|
47.0
|
1.0
|
C5
|
B:D16401
|
4.0
|
42.7
|
1.0
|
C2
|
B:UFP402
|
4.0
|
45.7
|
1.0
|
O
|
B:HOH518
|
4.2
|
54.3
|
1.0
|
OH
|
B:TYR135
|
4.3
|
58.8
|
1.0
|
N10
|
B:D16401
|
4.4
|
56.9
|
1.0
|
C4A
|
B:D16401
|
4.5
|
46.9
|
1.0
|
C8
|
B:D16401
|
4.6
|
47.2
|
1.0
|
O4'
|
B:UFP402
|
4.6
|
39.3
|
1.0
|
C1'
|
B:UFP402
|
4.7
|
41.1
|
1.0
|
CZ3
|
B:TRP109
|
4.7
|
58.8
|
1.0
|
CB
|
B:CYS195
|
4.7
|
68.3
|
1.0
|
C8A
|
B:D16401
|
4.8
|
47.0
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6zxo
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Fluorine Binding Sites List in 6zxo
Fluorine binding site 3 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F402
b:58.3
occ:1.00
|
F5
|
C:UFP402
|
0.0
|
58.3
|
1.0
|
C5
|
C:UFP402
|
1.3
|
41.9
|
1.0
|
C4
|
C:UFP402
|
2.4
|
42.1
|
1.0
|
C6
|
C:UFP402
|
2.4
|
39.3
|
1.0
|
O4
|
C:UFP402
|
2.6
|
40.4
|
1.0
|
SG
|
C:CYS195
|
3.5
|
93.7
|
1.0
|
N3
|
C:UFP402
|
3.6
|
40.3
|
1.0
|
N1
|
C:UFP402
|
3.6
|
35.5
|
1.0
|
CH2
|
C:TRP109
|
3.7
|
73.4
|
1.0
|
CP1
|
C:D16401
|
3.8
|
52.8
|
1.0
|
CD2
|
C:LEU192
|
3.8
|
74.2
|
1.0
|
CB
|
C:CYS195
|
3.8
|
67.6
|
1.0
|
OH
|
C:TYR135
|
4.0
|
78.5
|
1.0
|
C2
|
C:UFP402
|
4.0
|
39.8
|
1.0
|
CZ2
|
C:TRP109
|
4.1
|
78.8
|
1.0
|
C6
|
C:D16401
|
4.3
|
37.2
|
1.0
|
NE2
|
C:HIS196
|
4.5
|
77.7
|
1.0
|
C5
|
C:D16401
|
4.5
|
33.3
|
1.0
|
C9
|
C:D16401
|
4.6
|
40.4
|
1.0
|
C7
|
C:D16401
|
4.6
|
35.3
|
1.0
|
N10
|
C:D16401
|
4.7
|
45.5
|
1.0
|
CZ3
|
C:TRP109
|
4.8
|
67.1
|
1.0
|
CE2
|
C:TYR135
|
4.8
|
70.7
|
1.0
|
C1'
|
C:UFP402
|
4.9
|
34.9
|
1.0
|
CZ
|
C:TYR135
|
4.9
|
71.0
|
1.0
|
O4'
|
C:UFP402
|
4.9
|
38.5
|
1.0
|
C4A
|
C:D16401
|
4.9
|
31.0
|
1.0
|
N
|
C:CYS195
|
5.0
|
51.6
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6zxo
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Fluorine Binding Sites List in 6zxo
Fluorine binding site 4 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
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 His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F402
b:54.2
occ:1.00
|
F5
|
D:UFP402
|
0.0
|
54.2
|
1.0
|
C5
|
D:UFP402
|
1.4
|
45.1
|
1.0
|
C4
|
D:UFP402
|
2.4
|
46.6
|
1.0
|
C6
|
D:UFP402
|
2.4
|
42.9
|
1.0
|
O4
|
D:UFP402
|
2.7
|
49.6
|
1.0
|
CH2
|
D:TRP109
|
3.3
|
65.6
|
1.0
|
N3
|
D:UFP402
|
3.6
|
43.7
|
1.0
|
N1
|
D:UFP402
|
3.6
|
40.4
|
1.0
|
SG
|
D:CYS195
|
3.7
|
99.9
|
1.0
|
C6
|
D:D16401
|
3.7
|
49.6
|
1.0
|
CZ2
|
D:TRP109
|
3.8
|
65.1
|
1.0
|
C9
|
D:D16401
|
3.8
|
51.1
|
1.0
|
CP1
|
D:D16401
|
3.9
|
49.9
|
1.0
|
C5
|
D:D16401
|
4.0
|
43.3
|
1.0
|
C7
|
D:D16401
|
4.1
|
48.5
|
1.0
|
C2
|
D:UFP402
|
4.1
|
40.6
|
1.0
|
O
|
D:HOH534
|
4.2
|
46.9
|
1.0
|
N10
|
D:D16401
|
4.4
|
52.4
|
1.0
|
CD2
|
D:LEU192
|
4.5
|
67.9
|
1.0
|
CZ3
|
D:TRP109
|
4.5
|
69.1
|
1.0
|
OH
|
D:TYR135
|
4.5
|
86.9
|
1.0
|
C4A
|
D:D16401
|
4.6
|
39.9
|
1.0
|
C8
|
D:D16401
|
4.7
|
41.6
|
1.0
|
CB
|
D:CYS195
|
4.8
|
99.9
|
1.0
|
O4'
|
D:UFP402
|
4.9
|
41.1
|
1.0
|
C1'
|
D:UFP402
|
4.9
|
37.9
|
1.0
|
C8A
|
D:D16401
|
5.0
|
39.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6zxo
Go back to
Fluorine Binding Sites List in 6zxo
Fluorine binding site 5 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F402
b:64.9
occ:1.00
|
F5
|
E:UFP402
|
0.0
|
64.9
|
1.0
|
C5
|
E:UFP402
|
1.4
|
49.9
|
1.0
|
C6
|
E:UFP402
|
2.4
|
44.1
|
1.0
|
C4
|
E:UFP402
|
2.5
|
46.5
|
1.0
|
O4
|
E:UFP402
|
2.8
|
46.9
|
1.0
|
CH2
|
E:TRP109
|
3.3
|
61.7
|
1.0
|
N1
|
E:UFP402
|
3.6
|
40.0
|
1.0
|
N3
|
E:UFP402
|
3.7
|
43.9
|
1.0
|
CD2
|
E:LEU192
|
3.7
|
61.7
|
1.0
|
CZ2
|
E:TRP109
|
3.8
|
57.8
|
1.0
|
CP1
|
E:D16401
|
3.9
|
56.4
|
1.0
|
C6
|
E:D16401
|
4.0
|
41.6
|
1.0
|
SG
|
E:CYS195
|
4.0
|
76.7
|
1.0
|
C2
|
E:UFP402
|
4.1
|
40.9
|
1.0
|
CZ3
|
E:TRP109
|
4.1
|
64.6
|
1.0
|
C7
|
E:D16401
|
4.1
|
39.5
|
1.0
|
C5
|
E:D16401
|
4.2
|
40.4
|
1.0
|
OH
|
E:TYR135
|
4.3
|
56.6
|
1.0
|
C9
|
E:D16401
|
4.4
|
50.1
|
1.0
|
C8
|
E:D16401
|
4.5
|
38.5
|
1.0
|
C4A
|
E:D16401
|
4.5
|
42.0
|
1.0
|
O4'
|
E:UFP402
|
4.6
|
31.3
|
1.0
|
N10
|
E:D16401
|
4.6
|
57.1
|
1.0
|
C8A
|
E:D16401
|
4.6
|
38.7
|
1.0
|
C1'
|
E:UFP402
|
4.7
|
34.8
|
1.0
|
CB
|
E:CYS195
|
4.8
|
60.3
|
1.0
|
CG
|
E:LEU192
|
5.0
|
58.4
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6zxo
Go back to
Fluorine Binding Sites List in 6zxo
Fluorine binding site 6 out
of 6 in the Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex)
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of His-Tagged Human Thymidylate Synthase (Ht-Hts) in Complex with Fdump and Raltitrexed (Tomudex) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F402
b:68.2
occ:1.00
|
F5
|
F:UFP402
|
0.0
|
68.2
|
1.0
|
C5
|
F:UFP402
|
1.3
|
51.1
|
1.0
|
C6
|
F:UFP402
|
2.4
|
44.5
|
1.0
|
C4
|
F:UFP402
|
2.4
|
46.6
|
1.0
|
O4
|
F:UFP402
|
2.7
|
49.5
|
1.0
|
N1
|
F:UFP402
|
3.6
|
40.1
|
1.0
|
N3
|
F:UFP402
|
3.6
|
40.5
|
1.0
|
CP1
|
F:D16401
|
3.8
|
71.6
|
1.0
|
SG
|
F:CYS195
|
3.9
|
99.9
|
1.0
|
C6
|
F:D16401
|
3.9
|
55.9
|
1.0
|
OH
|
F:TYR135
|
4.0
|
73.4
|
1.0
|
C2
|
F:UFP402
|
4.0
|
39.4
|
1.0
|
C9
|
F:D16401
|
4.2
|
58.3
|
1.0
|
C5
|
F:D16401
|
4.2
|
51.5
|
1.0
|
CH2
|
F:TRP109
|
4.2
|
67.0
|
1.0
|
C7
|
F:D16401
|
4.2
|
60.9
|
1.0
|
CB
|
F:CYS195
|
4.4
|
76.6
|
1.0
|
N10
|
F:D16401
|
4.5
|
62.4
|
1.0
|
CZ2
|
F:TRP109
|
4.6
|
62.9
|
1.0
|
C4A
|
F:D16401
|
4.7
|
47.1
|
1.0
|
C8
|
F:D16401
|
4.7
|
54.7
|
1.0
|
O4'
|
F:UFP402
|
4.7
|
42.7
|
1.0
|
C1'
|
F:UFP402
|
4.8
|
40.4
|
1.0
|
C8A
|
F:D16401
|
4.9
|
48.8
|
1.0
|
CZ
|
F:TYR135
|
5.0
|
82.0
|
1.0
|
|
Reference:
C.Pozzi,
M.Santucci,
G.Marverti,
D.D'arca,
L.Tagliazucchi,
S.Ferrari,
G.Gozzi,
L.Losi,
G.Tassone,
S.Mangani,
G.Ponterini,
M.P.Costi.
Structural Bases For the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth By Drug Combinations. Cancers (Basel) V. 13 2021.
ISSN: ESSN 2072-6694
PubMed: 33923290
DOI: 10.3390/CANCERS13092061
Page generated: Fri Aug 2 05:27:11 2024
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