Fluorine in PDB 2yof: Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
Enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
All present enzymatic activity of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor:
2.7.4.9;
Protein crystallography data
The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor, PDB code: 2yof
was solved by
C.Huaqing,
J.Carrero-Lerida,
A.P.G.Silva,
J.L.Whittingham,
J.A.Brannigan,
L.M.Ruiz-Perez,
K.D.Read,
K.S.Wilson,
D.Gonzalez-Pacanowska,
I.H.Gilbert,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
94.95 /
1.82
|
|
Space group
|
P 31 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
109.639,
109.639,
121.892,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
18.856 /
23.086
|
Other elements in 2yof:
The structure of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
15;
Binding sites:
The binding sites of Fluorine atom in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
(pdb code 2yof). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 15 binding sites of Fluorine where determined in the
Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor, PDB code: 2yof:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 1 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:59.2
occ:0.50
|
FAF
|
A:74W211
|
0.0
|
59.2
|
0.5
|
|
FAF
|
A:74W211
|
0.9
|
33.0
|
0.5
|
|
CBE
|
A:74W211
|
1.3
|
59.0
|
0.5
|
|
CBE
|
A:74W211
|
2.1
|
32.5
|
0.5
|
|
FAH
|
A:74W211
|
2.2
|
59.8
|
0.5
|
|
FAG
|
A:74W211
|
2.2
|
59.5
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
57.9
|
0.5
|
|
OAD
|
A:74W211
|
2.6
|
14.0
|
0.5
|
|
OD2
|
A:ASP17
|
2.6
|
27.0
|
1.0
|
|
O
|
A:HOH2180
|
2.7
|
23.0
|
1.0
|
|
OAD
|
A:74W211
|
2.7
|
42.2
|
0.5
|
|
FAH
|
A:74W211
|
2.8
|
32.9
|
0.5
|
|
CAX
|
A:74W211
|
2.8
|
32.0
|
0.5
|
|
CAL
|
A:74W211
|
2.8
|
56.1
|
0.5
|
|
CG
|
A:ASP17
|
2.8
|
27.6
|
1.0
|
|
CAL
|
A:74W211
|
2.8
|
29.9
|
0.5
|
|
FAG
|
A:74W211
|
3.1
|
33.3
|
0.5
|
|
OD1
|
A:ASP17
|
3.1
|
30.6
|
1.0
|
|
CBA
|
A:74W211
|
3.4
|
42.5
|
0.5
|
|
CAN
|
A:74W211
|
3.4
|
45.6
|
0.5
|
|
CAW
|
A:74W211
|
3.6
|
57.5
|
0.5
|
|
CBA
|
A:74W211
|
3.7
|
11.8
|
0.5
|
|
CB
|
A:ASP17
|
3.7
|
26.9
|
1.0
|
|
CBB
|
A:74W211
|
3.7
|
43.3
|
0.5
|
|
OE1
|
A:GLU151
|
3.9
|
34.4
|
1.0
|
|
CAW
|
A:74W211
|
4.0
|
31.9
|
0.5
|
|
CAV
|
A:74W211
|
4.1
|
28.7
|
0.5
|
|
CB
|
A:TYR153
|
4.1
|
31.9
|
1.0
|
|
NE2
|
A:GLN159
|
4.2
|
32.1
|
1.0
|
|
CAV
|
A:74W211
|
4.2
|
54.7
|
0.5
|
|
C
|
A:TYR153
|
4.2
|
33.6
|
1.0
|
|
N
|
A:GLU154
|
4.3
|
35.2
|
1.0
|
|
CL
|
A:74W211
|
4.3
|
58.0
|
0.5
|
|
NAP
|
A:74W211
|
4.4
|
17.3
|
0.5
|
|
CBB
|
A:74W211
|
4.4
|
12.5
|
0.5
|
|
O
|
A:TYR153
|
4.5
|
33.1
|
1.0
|
|
CA
|
A:TYR153
|
4.6
|
32.4
|
1.0
|
|
CA
|
A:GLU154
|
4.6
|
37.5
|
1.0
|
|
CB
|
A:GLU151
|
4.6
|
35.8
|
1.0
|
|
N
|
A:TYR153
|
4.7
|
31.7
|
1.0
|
|
NAQ
|
A:74W211
|
4.8
|
25.7
|
0.5
|
|
CAK
|
A:74W211
|
4.8
|
56.9
|
0.5
|
|
NAP
|
A:74W211
|
4.8
|
47.4
|
0.5
|
|
CAT
|
A:74W211
|
4.8
|
22.5
|
0.5
|
|
CAO
|
A:74W211
|
4.9
|
41.8
|
0.5
|
|
CL
|
A:74W211
|
4.9
|
35.3
|
0.5
|
|
CAO
|
A:74W211
|
4.9
|
9.9
|
0.5
|
|
CD
|
A:GLU151
|
5.0
|
35.9
|
1.0
|
|
Fluorine binding site 2 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 2 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:59.5
occ:0.50
|
FAG
|
A:74W211
|
0.0
|
59.5
|
0.5
|
|
CBE
|
A:74W211
|
0.9
|
32.5
|
0.5
|
|
FAG
|
A:74W211
|
1.1
|
33.3
|
0.5
|
|
FAF
|
A:74W211
|
1.3
|
33.0
|
0.5
|
|
CBE
|
A:74W211
|
1.3
|
59.0
|
0.5
|
|
FAH
|
A:74W211
|
1.7
|
32.9
|
0.5
|
|
FAH
|
A:74W211
|
2.1
|
59.8
|
0.5
|
|
FAF
|
A:74W211
|
2.2
|
59.2
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
57.9
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
32.0
|
0.5
|
|
CL
|
A:74W211
|
2.7
|
58.0
|
0.5
|
|
CAW
|
A:74W211
|
2.8
|
57.5
|
0.5
|
|
CAL
|
A:74W211
|
3.2
|
29.9
|
0.5
|
|
CB
|
A:ASP17
|
3.4
|
26.9
|
1.0
|
|
CG
|
A:ASP17
|
3.4
|
27.6
|
1.0
|
|
CAW
|
A:74W211
|
3.4
|
31.9
|
0.5
|
|
OD2
|
A:ASP17
|
3.6
|
27.0
|
1.0
|
|
CA
|
A:GLU154
|
3.6
|
37.5
|
1.0
|
|
CAL
|
A:74W211
|
3.6
|
56.1
|
0.5
|
|
CL
|
A:74W211
|
3.7
|
35.3
|
0.5
|
|
NH2
|
A:ARG18
|
3.9
|
38.8
|
0.5
|
|
CG
|
A:GLU154
|
4.0
|
40.5
|
1.0
|
|
N
|
A:GLU154
|
4.0
|
35.2
|
1.0
|
|
CB
|
A:GLU154
|
4.0
|
37.3
|
1.0
|
|
OD1
|
A:ASP17
|
4.0
|
30.6
|
1.0
|
|
NH1
|
A:ARG18
|
4.0
|
38.9
|
0.5
|
|
NE2
|
A:GLN159
|
4.2
|
32.1
|
1.0
|
|
CAK
|
A:74W211
|
4.2
|
56.9
|
0.5
|
|
CZ
|
A:ARG18
|
4.3
|
38.9
|
0.5
|
|
O
|
A:HOH2180
|
4.3
|
23.0
|
1.0
|
|
C
|
A:TYR153
|
4.4
|
33.6
|
1.0
|
|
O
|
A:TYR153
|
4.5
|
33.1
|
1.0
|
|
CAV
|
A:74W211
|
4.6
|
28.7
|
0.5
|
|
C
|
A:GLU154
|
4.6
|
37.7
|
1.0
|
|
O
|
A:GLU154
|
4.7
|
38.6
|
1.0
|
|
OAD
|
A:74W211
|
4.7
|
14.0
|
0.5
|
|
CAK
|
A:74W211
|
4.7
|
31.3
|
0.5
|
|
CAV
|
A:74W211
|
4.8
|
54.7
|
0.5
|
|
OAD
|
A:74W211
|
4.8
|
42.2
|
0.5
|
|
CA
|
A:ASP17
|
4.8
|
26.2
|
1.0
|
|
CD
|
A:GLN159
|
5.0
|
34.9
|
1.0
|
|
CAJ
|
A:74W211
|
5.0
|
55.7
|
0.5
|
|
Fluorine binding site 3 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 3 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:59.8
occ:0.50
|
FAH
|
A:74W211
|
0.0
|
59.8
|
0.5
|
|
FAH
|
A:74W211
|
1.0
|
32.9
|
0.5
|
|
CBE
|
A:74W211
|
1.3
|
59.0
|
0.5
|
|
CBE
|
A:74W211
|
1.7
|
32.5
|
0.5
|
|
FAF
|
A:74W211
|
1.9
|
33.0
|
0.5
|
|
FAG
|
A:74W211
|
2.1
|
59.5
|
0.5
|
|
FAF
|
A:74W211
|
2.2
|
59.2
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
57.9
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
32.0
|
0.5
|
|
O
|
A:HOH2180
|
2.7
|
23.0
|
1.0
|
|
FAG
|
A:74W211
|
2.8
|
33.3
|
0.5
|
|
CB
|
A:GLU151
|
3.0
|
35.8
|
1.0
|
|
CAW
|
A:74W211
|
3.1
|
57.5
|
0.5
|
|
CAW
|
A:74W211
|
3.1
|
31.9
|
0.5
|
|
CL
|
A:74W211
|
3.2
|
58.0
|
0.5
|
|
N
|
A:GLU154
|
3.2
|
35.2
|
1.0
|
|
CL
|
A:74W211
|
3.2
|
35.3
|
0.5
|
|
CAL
|
A:74W211
|
3.4
|
56.1
|
0.5
|
|
CAL
|
A:74W211
|
3.4
|
29.9
|
0.5
|
|
CA
|
A:GLU154
|
3.4
|
37.5
|
1.0
|
|
CB
|
A:GLU154
|
3.6
|
37.3
|
1.0
|
|
OE1
|
A:GLU151
|
3.7
|
34.4
|
1.0
|
|
O
|
A:GLU151
|
3.7
|
34.8
|
1.0
|
|
C
|
A:GLU151
|
3.8
|
35.0
|
1.0
|
|
C
|
A:TYR153
|
3.8
|
33.6
|
1.0
|
|
CA
|
A:GLU151
|
3.8
|
35.9
|
1.0
|
|
N
|
A:TYR153
|
4.0
|
31.7
|
1.0
|
|
CG
|
A:GLU154
|
4.1
|
40.5
|
1.0
|
|
CG
|
A:GLU151
|
4.1
|
35.2
|
1.0
|
|
N
|
A:GLU151
|
4.3
|
37.7
|
1.0
|
|
CAK
|
A:74W211
|
4.3
|
31.3
|
0.5
|
|
CD
|
A:GLU151
|
4.3
|
35.9
|
1.0
|
|
CA
|
A:TYR153
|
4.3
|
32.4
|
1.0
|
|
CAK
|
A:74W211
|
4.4
|
56.9
|
0.5
|
|
OAD
|
A:74W211
|
4.4
|
14.0
|
0.5
|
|
N
|
A:ILE152
|
4.5
|
33.3
|
1.0
|
|
O
|
A:TYR153
|
4.5
|
33.1
|
1.0
|
|
CAV
|
A:74W211
|
4.5
|
28.7
|
0.5
|
|
OAD
|
A:74W211
|
4.6
|
42.2
|
0.5
|
|
OD2
|
A:ASP17
|
4.6
|
27.0
|
1.0
|
|
CB
|
A:TYR153
|
4.6
|
31.9
|
1.0
|
|
CAV
|
A:74W211
|
4.6
|
54.7
|
0.5
|
|
CAN
|
A:74W211
|
4.7
|
45.6
|
0.5
|
|
CG
|
A:ASP17
|
4.7
|
27.6
|
1.0
|
|
CD
|
A:GLU154
|
4.9
|
41.8
|
0.5
|
|
C
|
A:GLU154
|
4.9
|
37.7
|
1.0
|
|
CAJ
|
A:74W211
|
4.9
|
30.1
|
0.5
|
|
CAJ
|
A:74W211
|
5.0
|
55.7
|
0.5
|
|
C
|
A:ILE152
|
5.0
|
32.0
|
1.0
|
|
Fluorine binding site 4 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 4 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:33.0
occ:0.50
|
FAF
|
A:74W211
|
0.0
|
33.0
|
0.5
|
|
CBE
|
A:74W211
|
0.8
|
59.0
|
0.5
|
|
FAF
|
A:74W211
|
0.9
|
59.2
|
0.5
|
|
FAG
|
A:74W211
|
1.3
|
59.5
|
0.5
|
|
CBE
|
A:74W211
|
1.4
|
32.5
|
0.5
|
|
FAH
|
A:74W211
|
1.9
|
59.8
|
0.5
|
|
CAX
|
A:74W211
|
2.1
|
57.9
|
0.5
|
|
FAH
|
A:74W211
|
2.2
|
32.9
|
0.5
|
|
FAG
|
A:74W211
|
2.2
|
33.3
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
32.0
|
0.5
|
|
OD2
|
A:ASP17
|
2.8
|
27.0
|
1.0
|
|
CAL
|
A:74W211
|
2.8
|
29.9
|
0.5
|
|
CG
|
A:ASP17
|
2.8
|
27.6
|
1.0
|
|
CAL
|
A:74W211
|
3.0
|
56.1
|
0.5
|
|
CAW
|
A:74W211
|
3.2
|
57.5
|
0.5
|
|
O
|
A:HOH2180
|
3.3
|
23.0
|
1.0
|
|
OD1
|
A:ASP17
|
3.3
|
30.6
|
1.0
|
|
CB
|
A:ASP17
|
3.4
|
26.9
|
1.0
|
|
OAD
|
A:74W211
|
3.4
|
14.0
|
0.5
|
|
CL
|
A:74W211
|
3.6
|
58.0
|
0.5
|
|
OAD
|
A:74W211
|
3.6
|
42.2
|
0.5
|
|
CAW
|
A:74W211
|
3.7
|
31.9
|
0.5
|
|
NE2
|
A:GLN159
|
4.0
|
32.1
|
1.0
|
|
N
|
A:GLU154
|
4.1
|
35.2
|
1.0
|
|
CA
|
A:GLU154
|
4.1
|
37.5
|
1.0
|
|
CAN
|
A:74W211
|
4.1
|
45.6
|
0.5
|
|
C
|
A:TYR153
|
4.2
|
33.6
|
1.0
|
|
CAV
|
A:74W211
|
4.2
|
28.7
|
0.5
|
|
CBA
|
A:74W211
|
4.2
|
42.5
|
0.5
|
|
CAV
|
A:74W211
|
4.3
|
54.7
|
0.5
|
|
CL
|
A:74W211
|
4.3
|
35.3
|
0.5
|
|
O
|
A:TYR153
|
4.4
|
33.1
|
1.0
|
|
OE1
|
A:GLU151
|
4.4
|
34.4
|
1.0
|
|
CAK
|
A:74W211
|
4.4
|
56.9
|
0.5
|
|
CBA
|
A:74W211
|
4.5
|
11.8
|
0.5
|
|
CB
|
A:TYR153
|
4.6
|
31.9
|
1.0
|
|
CBB
|
A:74W211
|
4.6
|
43.3
|
0.5
|
|
CB
|
A:GLU154
|
4.7
|
37.3
|
1.0
|
|
CB
|
A:GLU151
|
4.7
|
35.8
|
1.0
|
|
CAK
|
A:74W211
|
4.8
|
31.3
|
0.5
|
|
CA
|
A:TYR153
|
4.8
|
32.4
|
1.0
|
|
CA
|
A:ASP17
|
4.8
|
26.2
|
1.0
|
|
CAJ
|
A:74W211
|
4.9
|
55.7
|
0.5
|
|
NAP
|
A:74W211
|
5.0
|
17.3
|
0.5
|
|
CG
|
A:GLU154
|
5.0
|
40.5
|
1.0
|
|
NAQ
|
A:74W211
|
5.0
|
25.7
|
0.5
|
|
Fluorine binding site 5 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 5 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:33.3
occ:0.50
|
FAG
|
A:74W211
|
0.0
|
33.3
|
0.5
|
|
FAG
|
A:74W211
|
1.1
|
59.5
|
0.5
|
|
CBE
|
A:74W211
|
1.3
|
32.5
|
0.5
|
|
CL
|
A:74W211
|
1.9
|
58.0
|
0.5
|
|
CBE
|
A:74W211
|
2.1
|
59.0
|
0.5
|
|
FAH
|
A:74W211
|
2.1
|
32.9
|
0.5
|
|
FAF
|
A:74W211
|
2.2
|
33.0
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
32.0
|
0.5
|
|
CAW
|
A:74W211
|
2.5
|
57.5
|
0.5
|
|
CAX
|
A:74W211
|
2.5
|
57.9
|
0.5
|
|
FAH
|
A:74W211
|
2.8
|
59.8
|
0.5
|
|
NH2
|
A:ARG18
|
2.9
|
38.8
|
0.5
|
|
FAF
|
A:74W211
|
3.1
|
59.2
|
0.5
|
|
CAW
|
A:74W211
|
3.2
|
31.9
|
0.5
|
|
CAL
|
A:74W211
|
3.3
|
29.9
|
0.5
|
|
CL
|
A:74W211
|
3.4
|
35.3
|
0.5
|
|
CZ
|
A:ARG18
|
3.4
|
38.9
|
0.5
|
|
NH1
|
A:ARG18
|
3.4
|
38.9
|
0.5
|
|
CB
|
A:ASP17
|
3.5
|
26.9
|
1.0
|
|
CAK
|
A:74W211
|
3.7
|
56.9
|
0.5
|
|
CG
|
A:GLU154
|
3.8
|
40.5
|
1.0
|
|
CAL
|
A:74W211
|
3.8
|
56.1
|
0.5
|
|
CG
|
A:ASP17
|
3.9
|
27.6
|
1.0
|
|
CA
|
A:GLU154
|
4.1
|
37.5
|
1.0
|
|
CB
|
A:GLU154
|
4.2
|
37.3
|
1.0
|
|
OD2
|
A:ASP17
|
4.3
|
27.0
|
1.0
|
|
OD1
|
A:ASP17
|
4.4
|
30.6
|
1.0
|
|
CAK
|
A:74W211
|
4.4
|
31.3
|
0.5
|
|
NE
|
A:ARG18
|
4.4
|
39.6
|
0.5
|
|
CAV
|
A:74W211
|
4.5
|
28.7
|
0.5
|
|
CAJ
|
A:74W211
|
4.7
|
55.7
|
0.5
|
|
CD
|
A:GLU154
|
4.7
|
41.8
|
0.5
|
|
CAV
|
A:74W211
|
4.8
|
54.7
|
0.5
|
|
N
|
A:GLU154
|
4.8
|
35.2
|
1.0
|
|
CA
|
A:ASP17
|
4.8
|
26.2
|
1.0
|
|
O
|
A:GLU154
|
4.9
|
38.6
|
1.0
|
|
NE2
|
A:GLN159
|
4.9
|
32.1
|
1.0
|
|
OE2
|
A:GLU154
|
5.0
|
42.4
|
0.5
|
|
CAJ
|
A:74W211
|
5.0
|
30.1
|
0.5
|
|
Fluorine binding site 6 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 6 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F211
b:32.9
occ:0.50
|
FAH
|
A:74W211
|
0.0
|
32.9
|
0.5
|
|
FAH
|
A:74W211
|
1.0
|
59.8
|
0.5
|
|
CBE
|
A:74W211
|
1.3
|
32.5
|
0.5
|
|
CBE
|
A:74W211
|
1.6
|
59.0
|
0.5
|
|
FAG
|
A:74W211
|
1.7
|
59.5
|
0.5
|
|
FAG
|
A:74W211
|
2.1
|
33.3
|
0.5
|
|
FAF
|
A:74W211
|
2.2
|
33.0
|
0.5
|
|
CL
|
A:74W211
|
2.3
|
58.0
|
0.5
|
|
CAX
|
A:74W211
|
2.4
|
32.0
|
0.5
|
|
CAX
|
A:74W211
|
2.5
|
57.9
|
0.5
|
|
CL
|
A:74W211
|
2.6
|
35.3
|
0.5
|
|
CAW
|
A:74W211
|
2.7
|
57.5
|
0.5
|
|
FAF
|
A:74W211
|
2.8
|
59.2
|
0.5
|
|
CAW
|
A:74W211
|
2.8
|
31.9
|
0.5
|
|
CB
|
A:GLU154
|
3.0
|
37.3
|
1.0
|
|
CA
|
A:GLU154
|
3.1
|
37.5
|
1.0
|
|
CG
|
A:GLU154
|
3.2
|
40.5
|
1.0
|
|
N
|
A:GLU154
|
3.3
|
35.2
|
1.0
|
|
CB
|
A:GLU151
|
3.5
|
35.8
|
1.0
|
|
CAL
|
A:74W211
|
3.6
|
29.9
|
0.5
|
|
O
|
A:HOH2180
|
3.7
|
23.0
|
1.0
|
|
CAL
|
A:74W211
|
3.8
|
56.1
|
0.5
|
|
O
|
A:GLU151
|
3.9
|
34.8
|
1.0
|
|
CD
|
A:GLU154
|
4.0
|
41.8
|
0.5
|
|
CAK
|
A:74W211
|
4.1
|
56.9
|
0.5
|
|
C
|
A:TYR153
|
4.1
|
33.6
|
1.0
|
|
CA
|
A:GLU151
|
4.2
|
35.9
|
1.0
|
|
CAK
|
A:74W211
|
4.2
|
31.3
|
0.5
|
|
C
|
A:GLU151
|
4.2
|
35.0
|
1.0
|
|
N
|
A:GLU151
|
4.2
|
37.7
|
1.0
|
|
NH2
|
A:ARG18
|
4.4
|
38.8
|
0.5
|
|
OE1
|
A:GLU154
|
4.4
|
42.5
|
0.5
|
|
OE1
|
A:GLU151
|
4.4
|
34.4
|
1.0
|
|
C
|
A:GLU154
|
4.5
|
37.7
|
1.0
|
|
CG
|
A:GLU151
|
4.6
|
35.2
|
1.0
|
|
O
|
A:TYR153
|
4.7
|
33.1
|
1.0
|
|
OE2
|
A:GLU154
|
4.7
|
42.4
|
0.5
|
|
N
|
A:TYR153
|
4.7
|
31.7
|
1.0
|
|
CAV
|
A:74W211
|
4.8
|
28.7
|
0.5
|
|
O
|
A:GLU154
|
4.8
|
38.6
|
1.0
|
|
CAV
|
A:74W211
|
4.9
|
54.7
|
0.5
|
|
OD2
|
A:ASP17
|
4.9
|
27.0
|
1.0
|
|
CG
|
A:ASP17
|
4.9
|
27.6
|
1.0
|
|
CD
|
A:GLU151
|
4.9
|
35.9
|
1.0
|
|
CA
|
A:TYR153
|
4.9
|
32.4
|
1.0
|
|
NH1
|
A:ARG18
|
4.9
|
38.9
|
0.5
|
|
CAJ
|
A:74W211
|
5.0
|
55.7
|
0.5
|
|
CAJ
|
A:74W211
|
5.0
|
30.1
|
0.5
|
|
Fluorine binding site 7 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 7 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F211
b:42.2
occ:0.70
|
FAF
|
B:74W211
|
0.0
|
42.2
|
0.7
|
|
CBE
|
B:74W211
|
1.3
|
42.1
|
0.7
|
|
FAH
|
B:74W211
|
2.1
|
41.5
|
0.7
|
|
FAG
|
B:74W211
|
2.2
|
42.6
|
0.7
|
|
CAX
|
B:74W211
|
2.4
|
41.5
|
0.7
|
|
CG
|
B:ASP17
|
2.6
|
27.9
|
1.0
|
|
OD2
|
B:ASP17
|
2.8
|
26.4
|
1.0
|
|
CAL
|
B:74W211
|
2.8
|
39.7
|
0.7
|
|
OD1
|
B:ASP17
|
3.0
|
29.4
|
1.0
|
|
CB
|
B:ASP17
|
3.2
|
27.8
|
1.0
|
|
O
|
B:HOH2190
|
3.3
|
25.3
|
1.0
|
|
OAD
|
B:74W211
|
3.4
|
20.3
|
1.0
|
|
CAW
|
B:74W211
|
3.7
|
42.8
|
0.7
|
|
NE2
|
B:GLN159
|
4.1
|
23.2
|
1.0
|
|
CA
|
B:GLU154
|
4.1
|
31.1
|
1.0
|
|
N
|
B:GLU154
|
4.1
|
29.1
|
1.0
|
|
OE1
|
B:GLU151
|
4.1
|
21.2
|
0.5
|
|
C
|
B:TYR153
|
4.2
|
27.8
|
1.0
|
|
CAV
|
B:74W211
|
4.2
|
39.4
|
0.7
|
|
CL
|
B:74W211
|
4.3
|
47.1
|
0.7
|
|
O
|
B:TYR153
|
4.4
|
27.4
|
1.0
|
|
CBA
|
B:74W211
|
4.4
|
19.6
|
1.0
|
|
CB
|
B:GLU154
|
4.6
|
31.6
|
1.0
|
|
CA
|
B:ASP17
|
4.6
|
27.7
|
1.0
|
|
CB
|
B:GLU151
|
4.7
|
29.9
|
0.5
|
|
CB
|
B:TYR153
|
4.7
|
26.2
|
1.0
|
|
CAK
|
B:74W211
|
4.8
|
41.0
|
0.7
|
|
O
|
B:HOH2192
|
4.9
|
50.5
|
1.0
|
|
CA
|
B:TYR153
|
4.9
|
26.9
|
1.0
|
|
NAP
|
B:74W211
|
4.9
|
30.3
|
1.0
|
|
CB
|
B:GLU151
|
5.0
|
31.0
|
0.5
|
|
Fluorine binding site 8 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 8 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F211
b:42.6
occ:0.70
|
FAG
|
B:74W211
|
0.0
|
42.6
|
0.7
|
|
CBE
|
B:74W211
|
1.3
|
42.1
|
0.7
|
|
FAH
|
B:74W211
|
2.1
|
41.5
|
0.7
|
|
FAF
|
B:74W211
|
2.2
|
42.2
|
0.7
|
|
CAX
|
B:74W211
|
2.4
|
41.5
|
0.7
|
|
CL
|
B:74W211
|
2.9
|
47.1
|
0.7
|
|
CAW
|
B:74W211
|
2.9
|
42.8
|
0.7
|
|
CAL
|
B:74W211
|
3.5
|
39.7
|
0.7
|
|
CB
|
B:GLU154
|
3.6
|
31.6
|
1.0
|
|
CA
|
B:GLU154
|
3.6
|
31.1
|
1.0
|
|
O
|
B:HOH2192
|
3.7
|
50.5
|
1.0
|
|
CB
|
B:ASP17
|
3.7
|
27.8
|
1.0
|
|
CG
|
B:ASP17
|
4.1
|
27.9
|
1.0
|
|
CAK
|
B:74W211
|
4.3
|
41.0
|
0.7
|
|
N
|
B:GLU154
|
4.4
|
29.1
|
1.0
|
|
O
|
B:HOH2186
|
4.4
|
53.4
|
1.0
|
|
OD1
|
B:ASP17
|
4.5
|
29.4
|
1.0
|
|
OD2
|
B:ASP17
|
4.5
|
26.4
|
1.0
|
|
O
|
B:GLU154
|
4.6
|
31.9
|
1.0
|
|
CAV
|
B:74W211
|
4.7
|
39.4
|
0.7
|
|
C
|
B:GLU154
|
4.7
|
31.2
|
1.0
|
|
CB
|
B:GLU151
|
4.9
|
29.9
|
0.5
|
|
O
|
B:HOH2190
|
5.0
|
25.3
|
1.0
|
|
CAJ
|
B:74W211
|
5.0
|
40.1
|
0.7
|
|
C
|
B:TYR153
|
5.0
|
27.8
|
1.0
|
|
Fluorine binding site 9 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 9 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F211
b:41.5
occ:0.70
|
FAH
|
B:74W211
|
0.0
|
41.5
|
0.7
|
|
CBE
|
B:74W211
|
1.3
|
42.1
|
0.7
|
|
FAG
|
B:74W211
|
2.1
|
42.6
|
0.7
|
|
FAF
|
B:74W211
|
2.1
|
42.2
|
0.7
|
|
CAX
|
B:74W211
|
2.4
|
41.5
|
0.7
|
|
CL
|
B:74W211
|
2.8
|
47.1
|
0.7
|
|
CAW
|
B:74W211
|
3.0
|
42.8
|
0.7
|
|
CB
|
B:GLU154
|
3.0
|
31.6
|
1.0
|
|
CB
|
B:GLU151
|
3.1
|
29.9
|
0.5
|
|
CA
|
B:GLU154
|
3.2
|
31.1
|
1.0
|
|
N
|
B:GLU154
|
3.3
|
29.1
|
1.0
|
|
O
|
B:HOH2190
|
3.3
|
25.3
|
1.0
|
|
CB
|
B:GLU151
|
3.5
|
31.0
|
0.5
|
|
CAL
|
B:74W211
|
3.5
|
39.7
|
0.7
|
|
O
|
B:GLU151
|
3.6
|
30.3
|
1.0
|
|
C
|
B:GLU151
|
3.8
|
30.1
|
1.0
|
|
CA
|
B:GLU151
|
3.9
|
30.6
|
0.5
|
|
OE1
|
B:GLU151
|
3.9
|
21.2
|
0.5
|
|
CA
|
B:GLU151
|
3.9
|
31.2
|
0.5
|
|
C
|
B:TYR153
|
4.0
|
27.8
|
1.0
|
|
N
|
B:GLU151
|
4.1
|
32.2
|
1.0
|
|
CG
|
B:GLU151
|
4.3
|
27.7
|
0.5
|
|
CAK
|
B:74W211
|
4.3
|
41.0
|
0.7
|
|
N
|
B:TYR153
|
4.3
|
26.6
|
1.0
|
|
CG
|
B:GLU151
|
4.4
|
31.0
|
0.5
|
|
CG
|
B:GLU154
|
4.5
|
35.8
|
1.0
|
|
CD
|
B:GLU151
|
4.5
|
25.3
|
0.5
|
|
O
|
B:TYR153
|
4.6
|
27.4
|
1.0
|
|
CA
|
B:TYR153
|
4.6
|
26.9
|
1.0
|
|
C
|
B:GLU154
|
4.7
|
31.2
|
1.0
|
|
N
|
B:ILE152
|
4.7
|
28.5
|
1.0
|
|
CAV
|
B:74W211
|
4.7
|
39.4
|
0.7
|
|
CG
|
B:ASP17
|
4.7
|
27.9
|
1.0
|
|
OD2
|
B:ASP17
|
4.8
|
26.4
|
1.0
|
|
OE1
|
B:GLU154
|
4.8
|
43.0
|
1.0
|
|
O
|
B:HOH2186
|
4.8
|
53.4
|
1.0
|
|
OAD
|
B:74W211
|
4.9
|
20.3
|
1.0
|
|
CD
|
B:GLU154
|
4.9
|
40.9
|
1.0
|
|
Fluorine binding site 10 out
of 15 in 2yof
Go back to
Fluorine Binding Sites List in 2yof
Fluorine binding site 10 out
of 15 in the Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Plasmodium Falciparum Thymidylate Kinase in Complex with A (Thio)Urea-Beta-Deoxythymidine Inhibitor within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F211
b:43.9
occ:0.50
|
FAF
|
C:74W211
|
0.0
|
43.9
|
0.5
|
|
CBE
|
C:74W211
|
1.3
|
43.5
|
0.5
|
|
FAH
|
C:74W211
|
2.2
|
44.2
|
0.5
|
|
FAG
|
C:74W211
|
2.2
|
43.6
|
0.5
|
|
CAX
|
C:74W211
|
2.3
|
42.6
|
0.5
|
|
CL
|
C:74W211
|
2.8
|
46.3
|
0.5
|
|
CAW
|
C:74W211
|
2.9
|
42.8
|
0.5
|
|
CAL
|
C:74W211
|
3.5
|
40.0
|
0.5
|
|
CAW
|
C:74W211
|
3.8
|
62.2
|
0.5
|
|
CAK
|
C:74W211
|
3.8
|
61.5
|
0.5
|
|
CL
|
C:74W211
|
4.1
|
63.5
|
0.5
|
|
CAK
|
C:74W211
|
4.2
|
41.3
|
0.5
|
|
CAX
|
C:74W211
|
4.4
|
62.2
|
0.5
|
|
CAJ
|
C:74W211
|
4.4
|
60.4
|
0.5
|
|
FAH
|
C:74W211
|
4.6
|
63.2
|
0.5
|
|
CAV
|
C:74W211
|
4.6
|
37.7
|
0.5
|
|
CAV
|
C:74W211
|
4.9
|
59.4
|
0.5
|
|
CAL
|
C:74W211
|
4.9
|
60.7
|
0.5
|
|
CAJ
|
C:74W211
|
4.9
|
39.6
|
0.5
|
|
Reference:
H.Cui,
J.Carrero-Lerida,
A.P.G.Silva,
J.L.Whittingham,
J.A.Brannigan,
L.M.Ruiz-Perez,
K.D.Read,
K.S.Wilson,
D.Gonzalez-Pacanowska,
I.H.Gilbert.
Synthesis and Evaluation of Alpha-Thymidine Analogues As Novel Antimalarials. J.Med.Chem. V. 55 10948 2012.
ISSN: ISSN 0022-2623
PubMed: 23240776
DOI: 10.1021/JM301328H
Page generated: Sun Dec 13 11:42:27 2020
|
