Fluorine in PDB 6pfg: Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid.
Protein crystallography data
The structure of Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid., PDB code: 6pfg
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)
|
48.64 /
2.71
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
213.635,
116.595,
221.411,
90.00,
95.21,
90.00
|
R / Rfree (%)
|
20.1 /
23.1
|
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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid.
(pdb code 6pfg). 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid., PDB code: 6pfg:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 6pfg
Go back to
Fluorine Binding Sites List in 6pfg
Fluorine binding site 1 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F602
b:81.3
occ:1.00
|
F5
|
A:UFP602
|
0.0
|
81.3
|
1.0
|
C5
|
A:UFP602
|
1.4
|
84.7
|
1.0
|
C6
|
A:UFP602
|
2.3
|
84.0
|
1.0
|
C4
|
A:UFP602
|
2.4
|
74.0
|
1.0
|
O4
|
A:UFP602
|
2.7
|
59.1
|
1.0
|
C6
|
A:OFJ603
|
3.2
|
83.2
|
1.0
|
C5
|
A:OFJ603
|
3.2
|
84.7
|
1.0
|
N1
|
A:UFP602
|
3.6
|
77.2
|
1.0
|
N3
|
A:UFP602
|
3.6
|
71.9
|
1.0
|
N3
|
A:OFJ603
|
3.6
|
90.1
|
1.0
|
C7
|
A:OFJ603
|
3.7
|
77.4
|
1.0
|
C2
|
A:OFJ603
|
3.7
|
95.3
|
1.0
|
OH
|
A:TYR342
|
4.0
|
72.5
|
1.0
|
C1
|
A:OFJ603
|
4.0
|
87.0
|
1.0
|
C2
|
A:UFP602
|
4.1
|
67.7
|
1.0
|
CZ2
|
A:TRP316
|
4.1
|
73.4
|
1.0
|
SG
|
A:CYS402
|
4.1
|
73.0
|
1.0
|
CH2
|
A:TRP316
|
4.1
|
79.0
|
1.0
|
CE2
|
A:TYR342
|
4.4
|
47.0
|
1.0
|
CB
|
A:CYS402
|
4.4
|
54.5
|
1.0
|
CZ
|
A:TYR342
|
4.6
|
45.7
|
1.0
|
O4'
|
A:UFP602
|
4.6
|
79.1
|
1.0
|
C3
|
A:OFJ603
|
4.7
|
91.4
|
1.0
|
CD2
|
A:LEU399
|
4.7
|
85.1
|
1.0
|
C1'
|
A:UFP602
|
4.7
|
71.2
|
1.0
|
N1
|
A:OFJ603
|
5.0
|
88.1
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 6pfg
Go back to
Fluorine Binding Sites List in 6pfg
Fluorine binding site 2 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F602
b:72.3
occ:1.00
|
F5
|
B:UFP602
|
0.0
|
72.3
|
1.0
|
C5
|
B:UFP602
|
1.4
|
66.1
|
1.0
|
C6
|
B:UFP602
|
2.3
|
62.1
|
1.0
|
C4
|
B:UFP602
|
2.4
|
67.0
|
1.0
|
O4
|
B:UFP602
|
2.7
|
61.8
|
1.0
|
C5
|
B:OFJ603
|
3.0
|
68.3
|
1.0
|
C6
|
B:OFJ603
|
3.1
|
68.3
|
1.0
|
C7
|
B:OFJ603
|
3.5
|
62.3
|
1.0
|
N3
|
B:OFJ603
|
3.6
|
70.5
|
1.0
|
N1
|
B:UFP602
|
3.6
|
60.3
|
1.0
|
C2
|
B:OFJ603
|
3.6
|
70.1
|
1.0
|
N3
|
B:UFP602
|
3.6
|
61.9
|
1.0
|
O
|
B:HOH727
|
3.9
|
41.4
|
1.0
|
C1
|
B:OFJ603
|
3.9
|
63.0
|
1.0
|
C2
|
B:UFP602
|
4.1
|
58.6
|
1.0
|
OH
|
B:TYR342
|
4.1
|
53.8
|
1.0
|
CZ2
|
B:TRP316
|
4.1
|
50.1
|
1.0
|
CH2
|
B:TRP316
|
4.1
|
48.9
|
1.0
|
SG
|
B:CYS402
|
4.1
|
61.9
|
1.0
|
O
|
B:HOH779
|
4.4
|
47.8
|
1.0
|
CD2
|
B:LEU399
|
4.5
|
44.0
|
1.0
|
CE2
|
B:TYR342
|
4.5
|
50.3
|
1.0
|
C3
|
B:OFJ603
|
4.5
|
67.3
|
1.0
|
CB
|
B:CYS402
|
4.5
|
45.0
|
1.0
|
O4'
|
B:UFP602
|
4.6
|
58.6
|
1.0
|
C1'
|
B:UFP602
|
4.7
|
53.0
|
1.0
|
CZ
|
B:TYR342
|
4.8
|
50.3
|
1.0
|
N1
|
B:OFJ603
|
4.9
|
71.0
|
1.0
|
O2
|
B:OFJ603
|
4.9
|
71.7
|
1.0
|
C8
|
B:OFJ603
|
4.9
|
53.9
|
1.0
|
CE2
|
B:TRP316
|
5.0
|
39.5
|
1.0
|
CZ3
|
B:TRP316
|
5.0
|
39.6
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 6pfg
Go back to
Fluorine Binding Sites List in 6pfg
Fluorine binding site 3 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F602
b:80.3
occ:1.00
|
F5
|
C:UFP602
|
0.0
|
80.3
|
1.0
|
C5
|
C:UFP602
|
1.4
|
70.1
|
1.0
|
C6
|
C:UFP602
|
2.3
|
70.1
|
1.0
|
C4
|
C:UFP602
|
2.4
|
62.1
|
1.0
|
O4
|
C:UFP602
|
2.7
|
65.5
|
1.0
|
O
|
C:HOH711
|
3.5
|
54.2
|
1.0
|
C6
|
C:OFJ603
|
3.6
|
75.4
|
1.0
|
C5
|
C:OFJ603
|
3.6
|
75.4
|
1.0
|
N1
|
C:UFP602
|
3.6
|
70.1
|
1.0
|
N3
|
C:UFP602
|
3.6
|
58.8
|
1.0
|
OH
|
C:TYR342
|
3.8
|
60.5
|
1.0
|
C7
|
C:OFJ603
|
3.9
|
78.9
|
1.0
|
SG
|
C:CYS402
|
4.0
|
61.0
|
1.0
|
N3
|
C:OFJ603
|
4.1
|
82.3
|
1.0
|
C2
|
C:UFP602
|
4.1
|
59.7
|
1.0
|
C2
|
C:OFJ603
|
4.1
|
86.9
|
1.0
|
CB
|
C:CYS402
|
4.1
|
48.1
|
1.0
|
CH2
|
C:TRP316
|
4.3
|
68.5
|
1.0
|
CZ2
|
C:TRP316
|
4.3
|
78.0
|
1.0
|
CE2
|
C:TYR342
|
4.3
|
46.0
|
1.0
|
C1
|
C:OFJ603
|
4.4
|
78.3
|
1.0
|
CZ
|
C:TYR342
|
4.5
|
41.7
|
1.0
|
O4'
|
C:UFP602
|
4.7
|
63.6
|
1.0
|
C1'
|
C:UFP602
|
4.8
|
69.5
|
1.0
|
CD2
|
C:HIS403
|
4.8
|
52.6
|
1.0
|
CD2
|
C:LEU399
|
4.9
|
74.4
|
1.0
|
NE2
|
C:HIS403
|
4.9
|
60.2
|
1.0
|
C3
|
C:OFJ603
|
5.0
|
75.7
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 6pfg
Go back to
Fluorine Binding Sites List in 6pfg
Fluorine binding site 4 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F602
b:99.5
occ:1.00
|
F5
|
D:UFP602
|
0.0
|
99.5
|
1.0
|
C5
|
D:UFP602
|
1.4
|
95.6
|
1.0
|
C6
|
D:UFP602
|
2.3
|
97.5
|
1.0
|
C4
|
D:UFP602
|
2.4
|
94.6
|
1.0
|
O4
|
D:UFP602
|
2.7
|
97.1
|
1.0
|
C5
|
D:OFJ603
|
3.3
|
0.1
|
1.0
|
C6
|
D:OFJ603
|
3.3
|
0.2
|
1.0
|
N1
|
D:UFP602
|
3.6
|
96.9
|
1.0
|
C7
|
D:OFJ603
|
3.6
|
98.2
|
1.0
|
N3
|
D:UFP602
|
3.6
|
93.0
|
1.0
|
C2
|
D:OFJ603
|
3.8
|
0.9
|
1.0
|
N3
|
D:OFJ603
|
3.8
|
0.3
|
1.0
|
CH2
|
D:TRP316
|
4.0
|
90.1
|
1.0
|
CZ2
|
D:TRP316
|
4.0
|
97.2
|
1.0
|
OH
|
D:TYR342
|
4.0
|
88.6
|
1.0
|
C1
|
D:OFJ603
|
4.1
|
0.4
|
1.0
|
C2
|
D:UFP602
|
4.1
|
91.5
|
1.0
|
SG
|
D:CYS402
|
4.3
|
96.6
|
1.0
|
CE2
|
D:TYR342
|
4.4
|
82.0
|
1.0
|
CB
|
D:CYS402
|
4.6
|
66.0
|
1.0
|
C3
|
D:OFJ603
|
4.6
|
0.9
|
1.0
|
O4'
|
D:UFP602
|
4.6
|
0.7
|
1.0
|
CZ
|
D:TYR342
|
4.6
|
78.7
|
1.0
|
CD2
|
D:LEU399
|
4.7
|
0.4
|
1.0
|
C1'
|
D:UFP602
|
4.7
|
94.8
|
1.0
|
CZ3
|
D:TRP316
|
4.9
|
93.8
|
1.0
|
CE2
|
D:TRP316
|
4.9
|
99.2
|
1.0
|
O2
|
D:OFJ603
|
5.0
|
0.4
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 6pfg
Go back to
Fluorine Binding Sites List in 6pfg
Fluorine binding site 5 out
of 5 in the Crystal Structure of Ts-Dhfr From Cryptosporidium Hominis in Complex with Nadph, Fdump and 2-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic 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-(4-((2-Amino-4-Oxo-4,7-Dihydro-3H-Pyrrolo[2, 3-D]Pyrimidin-5-Yl)Methyl)Benzamido)-4-Carbamoylbenzoic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F602
b:67.9
occ:1.00
|
F5
|
E:UFP602
|
0.0
|
67.9
|
1.0
|
C5
|
E:UFP602
|
1.4
|
63.5
|
1.0
|
C6
|
E:UFP602
|
2.3
|
62.9
|
1.0
|
C4
|
E:UFP602
|
2.4
|
55.6
|
1.0
|
O4
|
E:UFP602
|
2.7
|
40.0
|
1.0
|
C5
|
E:OFJ603
|
3.2
|
59.9
|
1.0
|
C6
|
E:OFJ603
|
3.2
|
55.3
|
1.0
|
C7
|
E:OFJ603
|
3.6
|
56.2
|
1.0
|
N1
|
E:UFP602
|
3.6
|
49.7
|
1.0
|
N3
|
E:UFP602
|
3.6
|
62.6
|
1.0
|
C2
|
E:OFJ603
|
3.6
|
67.5
|
1.0
|
O
|
E:HOH734
|
3.7
|
36.5
|
1.0
|
N3
|
E:OFJ603
|
3.7
|
70.0
|
1.0
|
C1
|
E:OFJ603
|
3.9
|
58.7
|
1.0
|
OH
|
E:TYR342
|
4.0
|
48.0
|
1.0
|
O
|
E:HOH826
|
4.1
|
46.7
|
1.0
|
C2
|
E:UFP602
|
4.1
|
47.0
|
1.0
|
SG
|
E:CYS402
|
4.1
|
52.3
|
1.0
|
CZ2
|
E:TRP316
|
4.2
|
36.0
|
1.0
|
CH2
|
E:TRP316
|
4.3
|
43.9
|
1.0
|
CB
|
E:CYS402
|
4.4
|
39.6
|
1.0
|
C3
|
E:OFJ603
|
4.5
|
65.8
|
1.0
|
CE2
|
E:TYR342
|
4.5
|
40.0
|
1.0
|
O4'
|
E:UFP602
|
4.6
|
49.7
|
1.0
|
CZ
|
E:TYR342
|
4.7
|
42.3
|
1.0
|
C1'
|
E:UFP602
|
4.7
|
46.4
|
1.0
|
CD2
|
E:LEU399
|
4.8
|
46.3
|
1.0
|
O2
|
E:OFJ603
|
4.9
|
63.3
|
1.0
|
N1
|
E:OFJ603
|
4.9
|
42.6
|
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
Page generated: Fri Aug 2 00:22:35 2024
|