Fluorine in PDB 6pfc: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
Protein crystallography data
The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid, PDB code: 6pfc
was solved by
D.J.Czyzyk,
M.Valhondo,
W.L.Jorgensen,
K.S.Anderson,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.56 /
2.69
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
214.982,
117.116,
221.798,
90.00,
95.26,
90.00
|
R / Rfree (%)
|
21.3 /
24
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
(pdb code 6pfc). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid, PDB code: 6pfc:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 6pfc
Go back to
Fluorine Binding Sites List in 6pfc
Fluorine binding site 1 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
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 Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F602
b:91.6
occ:1.00
|
F5
|
A:UFP602
|
0.0
|
91.6
|
1.0
|
C5
|
A:UFP602
|
1.4
|
84.0
|
1.0
|
C6
|
A:UFP602
|
2.3
|
83.9
|
1.0
|
C4
|
A:UFP602
|
2.4
|
85.7
|
1.0
|
O4
|
A:UFP602
|
2.7
|
85.9
|
1.0
|
C5
|
A:OED603
|
3.2
|
97.7
|
1.0
|
C6
|
A:OED603
|
3.3
|
93.6
|
1.0
|
C7
|
A:OED603
|
3.5
|
99.8
|
1.0
|
N1
|
A:UFP602
|
3.6
|
79.1
|
1.0
|
N3
|
A:UFP602
|
3.6
|
84.5
|
1.0
|
C2
|
A:OED603
|
3.8
|
97.2
|
1.0
|
N3
|
A:OED603
|
3.9
|
93.4
|
1.0
|
OH
|
A:TYR342
|
4.1
|
84.2
|
1.0
|
C2
|
A:UFP602
|
4.1
|
73.9
|
1.0
|
SG
|
A:CYS402
|
4.1
|
92.9
|
1.0
|
C1
|
A:OED603
|
4.2
|
92.5
|
1.0
|
CH2
|
A:TRP316
|
4.2
|
90.1
|
1.0
|
CZ2
|
A:TRP316
|
4.2
|
0.5
|
1.0
|
CB
|
A:CYS402
|
4.5
|
71.1
|
1.0
|
O4'
|
A:UFP602
|
4.6
|
92.2
|
1.0
|
CE2
|
A:TYR342
|
4.6
|
89.3
|
1.0
|
CD2
|
A:LEU399
|
4.7
|
94.8
|
1.0
|
C3
|
A:OED603
|
4.7
|
93.4
|
1.0
|
C1'
|
A:UFP602
|
4.7
|
87.3
|
1.0
|
CZ
|
A:TYR342
|
4.8
|
83.7
|
1.0
|
C8
|
A:OED603
|
5.0
|
93.7
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 6pfc
Go back to
Fluorine Binding Sites List in 6pfc
Fluorine binding site 2 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
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 Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F602
b:80.4
occ:1.00
|
F5
|
B:UFP602
|
0.0
|
80.4
|
1.0
|
C5
|
B:UFP602
|
1.4
|
77.0
|
1.0
|
C6
|
B:UFP602
|
2.3
|
73.3
|
1.0
|
C4
|
B:UFP602
|
2.4
|
73.4
|
1.0
|
O4
|
B:UFP602
|
2.7
|
67.5
|
1.0
|
C5
|
B:OED603
|
3.2
|
77.7
|
1.0
|
C6
|
B:OED603
|
3.4
|
78.4
|
1.0
|
C7
|
B:OED603
|
3.5
|
68.4
|
1.0
|
N1
|
B:UFP602
|
3.6
|
67.4
|
1.0
|
N3
|
B:UFP602
|
3.6
|
70.8
|
1.0
|
C2
|
B:OED603
|
3.8
|
81.9
|
1.0
|
N3
|
B:OED603
|
3.9
|
72.3
|
1.0
|
C2
|
B:UFP602
|
4.1
|
65.7
|
1.0
|
SG
|
B:CYS402
|
4.1
|
71.6
|
1.0
|
C1
|
B:OED603
|
4.2
|
75.0
|
1.0
|
CZ2
|
B:TRP316
|
4.2
|
65.5
|
1.0
|
CH2
|
B:TRP316
|
4.2
|
70.7
|
1.0
|
OH
|
B:TYR342
|
4.2
|
70.6
|
1.0
|
O
|
B:HOH743
|
4.4
|
59.7
|
1.0
|
CB
|
B:CYS402
|
4.5
|
58.6
|
1.0
|
O4'
|
B:UFP602
|
4.6
|
69.3
|
1.0
|
C3
|
B:OED603
|
4.6
|
74.2
|
1.0
|
CE2
|
B:TYR342
|
4.7
|
54.3
|
1.0
|
C1'
|
B:UFP602
|
4.7
|
66.2
|
1.0
|
CD2
|
B:LEU399
|
4.8
|
75.2
|
1.0
|
CZ
|
B:TYR342
|
4.9
|
49.7
|
1.0
|
O1
|
B:OED603
|
4.9
|
69.0
|
1.0
|
C8
|
B:OED603
|
4.9
|
69.6
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 6pfc
Go back to
Fluorine Binding Sites List in 6pfc
Fluorine binding site 3 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
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 Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F602
b:77.4
occ:1.00
|
F5
|
C:UFP602
|
0.0
|
77.4
|
1.0
|
C5
|
C:UFP602
|
1.4
|
77.1
|
1.0
|
C6
|
C:UFP602
|
2.3
|
71.8
|
1.0
|
C4
|
C:UFP602
|
2.4
|
68.1
|
1.0
|
O4
|
C:UFP602
|
2.8
|
65.3
|
1.0
|
C5
|
C:OED603
|
3.1
|
71.7
|
1.0
|
C6
|
C:OED603
|
3.2
|
69.5
|
1.0
|
C7
|
C:OED603
|
3.4
|
65.6
|
1.0
|
N1
|
C:UFP602
|
3.6
|
65.4
|
1.0
|
N3
|
C:UFP602
|
3.6
|
61.9
|
1.0
|
C2
|
C:OED603
|
3.7
|
77.4
|
1.0
|
N3
|
C:OED603
|
3.8
|
70.0
|
1.0
|
C1
|
C:OED603
|
4.1
|
62.3
|
1.0
|
C2
|
C:UFP602
|
4.1
|
64.5
|
1.0
|
SG
|
C:CYS402
|
4.2
|
67.7
|
1.0
|
OH
|
C:TYR342
|
4.2
|
69.1
|
1.0
|
CH2
|
C:TRP316
|
4.4
|
58.1
|
1.0
|
CZ2
|
C:TRP316
|
4.4
|
69.2
|
1.0
|
CB
|
C:CYS402
|
4.6
|
62.1
|
1.0
|
C3
|
C:OED603
|
4.6
|
71.3
|
1.0
|
O4'
|
C:UFP602
|
4.6
|
65.7
|
1.0
|
CD2
|
C:LEU399
|
4.6
|
67.1
|
1.0
|
CE2
|
C:TYR342
|
4.6
|
61.0
|
1.0
|
C1'
|
C:UFP602
|
4.7
|
61.6
|
1.0
|
CZ
|
C:TYR342
|
4.8
|
52.8
|
1.0
|
C8
|
C:OED603
|
4.9
|
60.1
|
1.0
|
O1
|
C:OED603
|
4.9
|
75.0
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 6pfc
Go back to
Fluorine Binding Sites List in 6pfc
Fluorine binding site 4 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
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 Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F602
b:73.7
occ:1.00
|
F5
|
D:UFP602
|
0.0
|
73.7
|
1.0
|
C5
|
D:UFP602
|
1.4
|
64.4
|
1.0
|
C6
|
D:UFP602
|
2.3
|
60.5
|
1.0
|
C4
|
D:UFP602
|
2.4
|
59.4
|
1.0
|
O4
|
D:UFP602
|
2.7
|
63.6
|
1.0
|
C5
|
D:OED603
|
3.1
|
60.5
|
1.0
|
C6
|
D:OED603
|
3.2
|
64.2
|
1.0
|
C7
|
D:OED603
|
3.4
|
65.7
|
1.0
|
N1
|
D:UFP602
|
3.6
|
59.1
|
1.0
|
N3
|
D:UFP602
|
3.6
|
65.7
|
1.0
|
O
|
D:HOH738
|
3.7
|
44.8
|
1.0
|
C2
|
D:OED603
|
3.7
|
64.3
|
1.0
|
N3
|
D:OED603
|
3.8
|
65.8
|
1.0
|
C2
|
D:UFP602
|
4.1
|
62.5
|
1.0
|
C1
|
D:OED603
|
4.1
|
59.6
|
1.0
|
CZ2
|
D:TRP316
|
4.2
|
53.2
|
1.0
|
OH
|
D:TYR342
|
4.2
|
62.0
|
1.0
|
SG
|
D:CYS402
|
4.2
|
65.1
|
1.0
|
CH2
|
D:TRP316
|
4.2
|
54.5
|
1.0
|
O
|
D:HOH757
|
4.3
|
47.0
|
1.0
|
CB
|
D:CYS402
|
4.5
|
55.8
|
1.0
|
CD2
|
D:LEU399
|
4.6
|
56.8
|
1.0
|
O4'
|
D:UFP602
|
4.6
|
57.4
|
1.0
|
C3
|
D:OED603
|
4.6
|
66.5
|
1.0
|
CE2
|
D:TYR342
|
4.6
|
53.8
|
1.0
|
C1'
|
D:UFP602
|
4.7
|
54.9
|
1.0
|
CZ
|
D:TYR342
|
4.8
|
54.5
|
1.0
|
C8
|
D:OED603
|
4.8
|
59.0
|
1.0
|
O1
|
D:OED603
|
4.9
|
65.2
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 6pfc
Go back to
Fluorine Binding Sites List in 6pfc
Fluorine binding site 5 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid
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 Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H- Pyrrolo[2,3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Methoxyphenyl)Acetic Acid within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F602
b:69.0
occ:1.00
|
F5
|
E:UFP602
|
0.0
|
69.0
|
1.0
|
C5
|
E:UFP602
|
1.4
|
63.2
|
1.0
|
C6
|
E:UFP602
|
2.3
|
57.6
|
1.0
|
C4
|
E:UFP602
|
2.4
|
59.5
|
1.0
|
O4
|
E:UFP602
|
2.7
|
60.2
|
1.0
|
C5
|
E:OED603
|
3.2
|
56.6
|
1.0
|
C6
|
E:OED603
|
3.2
|
56.9
|
1.0
|
C7
|
E:OED603
|
3.5
|
67.0
|
1.0
|
O
|
E:HOH730
|
3.5
|
44.2
|
1.0
|
N1
|
E:UFP602
|
3.6
|
50.5
|
1.0
|
N3
|
E:UFP602
|
3.6
|
62.9
|
1.0
|
C2
|
E:OED603
|
3.7
|
64.5
|
1.0
|
N3
|
E:OED603
|
3.8
|
60.5
|
1.0
|
C1
|
E:OED603
|
4.1
|
56.3
|
1.0
|
C2
|
E:UFP602
|
4.1
|
54.6
|
1.0
|
SG
|
E:CYS402
|
4.1
|
56.3
|
1.0
|
OH
|
E:TYR342
|
4.1
|
56.5
|
1.0
|
CH2
|
E:TRP316
|
4.1
|
51.0
|
1.0
|
CZ2
|
E:TRP316
|
4.2
|
50.2
|
1.0
|
O
|
E:HOH783
|
4.4
|
50.8
|
1.0
|
CB
|
E:CYS402
|
4.4
|
52.1
|
1.0
|
CE2
|
E:TYR342
|
4.6
|
50.0
|
1.0
|
C3
|
E:OED603
|
4.6
|
64.4
|
1.0
|
O4'
|
E:UFP602
|
4.7
|
51.1
|
1.0
|
C1'
|
E:UFP602
|
4.7
|
48.4
|
1.0
|
CD2
|
E:LEU399
|
4.8
|
57.2
|
1.0
|
CZ
|
E:TYR342
|
4.8
|
51.9
|
1.0
|
O1
|
E:OED603
|
4.9
|
65.7
|
1.0
|
C8
|
E:OED603
|
5.0
|
54.7
|
1.0
|
|
Reference:
D.J.Czyzyk,
M.Valhondo,
L.Deiana,
J.Tirado-Rives,
W.L.Jorgensen,
K.S.Anderson.
Structure Activity Relationship Towards Design of Cryptosporidium Specific Thymidylate Synthase Inhibitors. Eur.J.Med.Chem. V. 183 11673 2019.
ISSN: ISSN 0223-5234
PubMed: 31536894
DOI: 10.1016/J.EJMECH.2019.111673
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