Fluorine in PDB 1xor: Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
Enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
All present enzymatic activity of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine:
3.1.4.17;
Protein crystallography data
The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine, PDB code: 1xor
was solved by
G.L.Card,
B.P.England,
Y.Suzuki,
D.Fong,
B.Powell,
B.Lee,
C.Luu,
M.Tabrizizad,
S.Gillette,
P.N.Ibrahim,
D.R.Artis,
G.Bollag,
M.V.Milburn,
S.-H.Kim,
J.Schlessinger,
K.Y.J.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
81.65 /
1.54
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.279,
78.401,
163.471,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.8 /
19.5
|
Other elements in 1xor:
The structure of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine also contains other interesting chemical elements:
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
(pdb code 1xor). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine, PDB code: 1xor:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 1 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:22.8
occ:0.45
|
F16
|
A:ZAR701
|
0.0
|
22.8
|
0.5
|
|
F17
|
A:ZAR701
|
0.9
|
21.0
|
0.4
|
|
C19
|
A:ZAR701
|
1.1
|
22.1
|
0.2
|
|
C14
|
A:ZAR701
|
1.4
|
22.1
|
0.5
|
|
C14
|
A:ZAR701
|
1.6
|
21.5
|
0.4
|
|
F16
|
A:ZAR701
|
2.0
|
20.8
|
0.4
|
|
O18
|
A:ZAR701
|
2.2
|
21.6
|
0.2
|
|
F17
|
A:ZAR701
|
2.2
|
23.9
|
0.5
|
|
O15
|
A:ZAR701
|
2.2
|
19.6
|
0.4
|
|
O15
|
A:ZAR701
|
2.3
|
18.9
|
0.5
|
|
C12
|
A:ZAR701
|
2.8
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
2.8
|
19.6
|
0.4
|
|
C10
|
A:ZAR701
|
2.8
|
22.4
|
0.2
|
|
C9
|
A:ZAR701
|
2.8
|
22.8
|
0.2
|
|
C11
|
A:ZAR701
|
2.9
|
18.8
|
0.5
|
|
C12
|
A:ZAR701
|
2.9
|
18.2
|
0.5
|
|
SD
|
A:MET357
|
3.6
|
18.2
|
1.0
|
|
CG
|
A:PHE372
|
3.7
|
10.8
|
1.0
|
|
CD1
|
A:PHE372
|
3.7
|
12.1
|
1.0
|
|
CB
|
A:PHE372
|
3.8
|
10.1
|
1.0
|
|
CE
|
A:MET357
|
3.8
|
18.6
|
1.0
|
|
O
|
A:HOH1226
|
4.0
|
39.9
|
1.0
|
|
C13
|
A:ZAR701
|
4.1
|
19.2
|
0.4
|
|
O
|
A:HOH1102
|
4.1
|
30.0
|
1.0
|
|
C10
|
A:ZAR701
|
4.2
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
4.2
|
22.3
|
0.2
|
|
C10
|
A:ZAR701
|
4.2
|
18.4
|
0.5
|
|
CD2
|
A:PHE372
|
4.2
|
11.0
|
1.0
|
|
C8
|
A:ZAR701
|
4.2
|
23.6
|
0.2
|
|
C13
|
A:ZAR701
|
4.2
|
18.1
|
0.5
|
|
CE1
|
A:PHE372
|
4.3
|
12.0
|
1.0
|
|
CE2
|
A:PHE340
|
4.4
|
11.9
|
1.0
|
|
O
|
A:SER368
|
4.5
|
9.0
|
1.0
|
|
NE2
|
A:GLN369
|
4.6
|
11.0
|
1.0
|
|
N4
|
A:ZAR701
|
4.6
|
25.0
|
0.2
|
|
O15
|
A:ZAR701
|
4.7
|
22.0
|
0.2
|
|
O18
|
A:ZAR701
|
4.7
|
19.1
|
0.5
|
|
O18
|
A:ZAR701
|
4.7
|
19.6
|
0.4
|
|
CE2
|
A:PHE372
|
4.7
|
11.9
|
1.0
|
|
CZ
|
A:PHE372
|
4.8
|
12.3
|
1.0
|
|
CZ
|
A:PHE340
|
4.8
|
11.7
|
1.0
|
|
C5
|
A:ZAR701
|
4.9
|
24.5
|
0.2
|
|
CA
|
A:PHE372
|
4.9
|
9.8
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 2 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:20.8
occ:0.38
|
F16
|
A:ZAR701
|
0.0
|
20.8
|
0.4
|
|
C14
|
A:ZAR701
|
1.1
|
22.1
|
0.5
|
|
F17
|
A:ZAR701
|
1.3
|
23.9
|
0.5
|
|
C14
|
A:ZAR701
|
1.4
|
21.5
|
0.4
|
|
C19
|
A:ZAR701
|
1.5
|
22.1
|
0.2
|
|
F16
|
A:ZAR701
|
2.0
|
22.8
|
0.5
|
|
F17
|
A:ZAR701
|
2.2
|
21.0
|
0.4
|
|
O15
|
A:ZAR701
|
2.2
|
19.6
|
0.4
|
|
O18
|
A:ZAR701
|
2.3
|
21.6
|
0.2
|
|
O15
|
A:ZAR701
|
2.3
|
18.9
|
0.5
|
|
NE2
|
A:GLN369
|
3.1
|
11.0
|
1.0
|
|
O
|
A:SER368
|
3.1
|
9.0
|
1.0
|
|
CB
|
A:PHE372
|
3.4
|
10.1
|
1.0
|
|
C
|
A:SER368
|
3.5
|
9.0
|
1.0
|
|
C11
|
A:ZAR701
|
3.5
|
19.6
|
0.4
|
|
C10
|
A:ZAR701
|
3.6
|
22.4
|
0.2
|
|
C11
|
A:ZAR701
|
3.6
|
18.8
|
0.5
|
|
O
|
A:HOH1069
|
3.7
|
23.4
|
1.0
|
|
SD
|
A:MET357
|
3.8
|
18.2
|
1.0
|
|
CG
|
A:PHE372
|
3.8
|
10.8
|
1.0
|
|
CD
|
A:GLN369
|
3.9
|
9.6
|
1.0
|
|
CB
|
A:SER368
|
3.9
|
9.5
|
1.0
|
|
O
|
A:HOH1102
|
3.9
|
30.0
|
1.0
|
|
N
|
A:GLN369
|
3.9
|
8.7
|
1.0
|
|
CA
|
A:GLN369
|
4.1
|
8.5
|
1.0
|
|
CD2
|
A:PHE372
|
4.1
|
11.0
|
1.0
|
|
C12
|
A:ZAR701
|
4.2
|
19.1
|
0.4
|
|
CA
|
A:SER368
|
4.3
|
9.4
|
1.0
|
|
C9
|
A:ZAR701
|
4.3
|
22.8
|
0.2
|
|
C12
|
A:ZAR701
|
4.3
|
18.2
|
0.5
|
|
OE1
|
A:GLN369
|
4.4
|
9.6
|
1.0
|
|
CD1
|
A:PHE372
|
4.5
|
12.1
|
1.0
|
|
O15
|
A:ZAR701
|
4.5
|
22.0
|
0.2
|
|
O18
|
A:ZAR701
|
4.5
|
19.6
|
0.4
|
|
O18
|
A:ZAR701
|
4.6
|
19.1
|
0.5
|
|
C10
|
A:ZAR701
|
4.6
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
4.6
|
22.3
|
0.2
|
|
C10
|
A:ZAR701
|
4.6
|
18.4
|
0.5
|
|
CA
|
A:PHE372
|
4.6
|
9.8
|
1.0
|
|
CG
|
A:GLN369
|
4.7
|
8.9
|
1.0
|
|
CE
|
A:MET357
|
4.8
|
18.6
|
1.0
|
|
O
|
A:HOH1226
|
4.8
|
39.9
|
1.0
|
|
N
|
A:PHE372
|
4.8
|
9.7
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 3 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:21.6
occ:0.17
|
F16
|
A:ZAR701
|
0.0
|
21.6
|
0.2
|
|
C14
|
A:ZAR701
|
1.4
|
22.1
|
0.2
|
|
C19
|
A:ZAR701
|
1.9
|
20.1
|
0.5
|
|
C19
|
A:ZAR701
|
1.9
|
20.4
|
0.4
|
|
F17
|
A:ZAR701
|
2.2
|
21.9
|
0.2
|
|
O18
|
A:ZAR701
|
2.2
|
19.1
|
0.5
|
|
O18
|
A:ZAR701
|
2.2
|
19.6
|
0.4
|
|
O15
|
A:ZAR701
|
2.3
|
22.0
|
0.2
|
|
C10
|
A:ZAR701
|
3.2
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
3.2
|
22.3
|
0.2
|
|
C10
|
A:ZAR701
|
3.3
|
18.4
|
0.5
|
|
OE1
|
A:GLN369
|
3.4
|
9.6
|
1.0
|
|
CE2
|
A:PHE372
|
3.4
|
11.9
|
1.0
|
|
CG
|
A:PRO322
|
3.4
|
8.6
|
1.0
|
|
CE1
|
A:TYR329
|
3.4
|
6.9
|
1.0
|
|
CB
|
A:ASN321
|
3.5
|
9.5
|
1.0
|
|
CD
|
A:PRO322
|
3.6
|
8.5
|
1.0
|
|
C9
|
A:ZAR701
|
3.7
|
19.0
|
0.4
|
|
C12
|
A:ZAR701
|
3.7
|
22.7
|
0.2
|
|
OD1
|
A:ASN321
|
3.8
|
12.1
|
1.0
|
|
C9
|
A:ZAR701
|
3.8
|
18.1
|
0.5
|
|
CD2
|
A:PHE372
|
3.9
|
11.0
|
1.0
|
|
CD1
|
A:TYR329
|
4.1
|
6.6
|
1.0
|
|
CG
|
A:ASN321
|
4.1
|
11.6
|
1.0
|
|
CD
|
A:GLN369
|
4.2
|
9.6
|
1.0
|
|
N
|
A:PRO322
|
4.2
|
8.2
|
1.0
|
|
C11
|
A:ZAR701
|
4.2
|
19.6
|
0.4
|
|
O
|
A:HOH1017
|
4.3
|
15.5
|
1.0
|
|
NE2
|
A:GLN369
|
4.3
|
11.0
|
1.0
|
|
C10
|
A:ZAR701
|
4.3
|
22.4
|
0.2
|
|
O15
|
A:ZAR701
|
4.4
|
19.6
|
0.4
|
|
C11
|
A:ZAR701
|
4.4
|
18.8
|
0.5
|
|
CZ
|
A:TYR329
|
4.5
|
6.8
|
1.0
|
|
O15
|
A:ZAR701
|
4.5
|
18.9
|
0.5
|
|
CZ
|
A:PHE372
|
4.5
|
12.3
|
1.0
|
|
OG1
|
A:THR333
|
4.5
|
9.2
|
1.0
|
|
O18
|
A:ZAR701
|
4.6
|
21.6
|
0.2
|
|
CA
|
A:ASN321
|
4.6
|
9.0
|
1.0
|
|
C
|
A:ASN321
|
4.6
|
8.4
|
1.0
|
|
OH
|
A:TYR329
|
4.6
|
8.0
|
1.0
|
|
CB
|
A:PRO322
|
4.7
|
8.2
|
1.0
|
|
CA
|
A:PRO322
|
4.9
|
8.1
|
1.0
|
|
C8
|
A:ZAR701
|
5.0
|
19.0
|
0.4
|
|
Fluorine binding site 4 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 4 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:23.9
occ:0.45
|
F17
|
A:ZAR701
|
0.0
|
23.9
|
0.5
|
|
C14
|
A:ZAR701
|
1.0
|
21.5
|
0.4
|
|
F16
|
A:ZAR701
|
1.3
|
20.8
|
0.4
|
|
C19
|
A:ZAR701
|
1.4
|
22.1
|
0.2
|
|
C14
|
A:ZAR701
|
1.4
|
22.1
|
0.5
|
|
F17
|
A:ZAR701
|
1.8
|
21.0
|
0.4
|
|
F16
|
A:ZAR701
|
2.2
|
22.8
|
0.5
|
|
O18
|
A:ZAR701
|
2.2
|
21.6
|
0.2
|
|
O15
|
A:ZAR701
|
2.2
|
18.9
|
0.5
|
|
O15
|
A:ZAR701
|
2.4
|
19.6
|
0.4
|
|
NE2
|
A:GLN369
|
3.2
|
11.0
|
1.0
|
|
SD
|
A:MET357
|
3.3
|
18.2
|
1.0
|
|
O
|
A:HOH1069
|
3.3
|
23.4
|
1.0
|
|
C11
|
A:ZAR701
|
3.4
|
18.8
|
0.5
|
|
C10
|
A:ZAR701
|
3.5
|
22.4
|
0.2
|
|
C11
|
A:ZAR701
|
3.5
|
19.6
|
0.4
|
|
CB
|
A:SER368
|
3.8
|
9.5
|
1.0
|
|
C12
|
A:ZAR701
|
4.0
|
18.2
|
0.5
|
|
O
|
A:SER368
|
4.1
|
9.0
|
1.0
|
|
C9
|
A:ZAR701
|
4.1
|
22.8
|
0.2
|
|
C12
|
A:ZAR701
|
4.1
|
19.1
|
0.4
|
|
CE2
|
A:PHE340
|
4.2
|
11.9
|
1.0
|
|
C
|
A:SER368
|
4.2
|
9.0
|
1.0
|
|
CD
|
A:GLN369
|
4.3
|
9.6
|
1.0
|
|
CE
|
A:MET357
|
4.3
|
18.6
|
1.0
|
|
SD
|
A:MET337
|
4.4
|
15.2
|
1.0
|
|
O15
|
A:ZAR701
|
4.5
|
22.0
|
0.2
|
|
C11
|
A:ZAR701
|
4.5
|
22.3
|
0.2
|
|
C10
|
A:ZAR701
|
4.5
|
18.4
|
0.5
|
|
C10
|
A:ZAR701
|
4.5
|
19.1
|
0.4
|
|
O
|
A:HOH1102
|
4.6
|
30.0
|
1.0
|
|
O18
|
A:ZAR701
|
4.6
|
19.6
|
0.4
|
|
O18
|
A:ZAR701
|
4.6
|
19.1
|
0.5
|
|
N
|
A:GLN369
|
4.6
|
8.7
|
1.0
|
|
CB
|
A:PHE372
|
4.6
|
10.1
|
1.0
|
|
CA
|
A:SER368
|
4.6
|
9.4
|
1.0
|
|
CG
|
A:MET357
|
4.7
|
16.0
|
1.0
|
|
OG
|
A:SER368
|
4.8
|
12.6
|
1.0
|
|
CG
|
A:PHE372
|
4.9
|
10.8
|
1.0
|
|
CD2
|
A:PHE340
|
4.9
|
10.9
|
1.0
|
|
CG2
|
A:ILE336
|
4.9
|
8.0
|
1.0
|
|
CA
|
A:GLN369
|
4.9
|
8.5
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 5 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:21.0
occ:0.38
|
F17
|
A:ZAR701
|
0.0
|
21.0
|
0.4
|
|
C19
|
A:ZAR701
|
0.9
|
22.1
|
0.2
|
|
F16
|
A:ZAR701
|
0.9
|
22.8
|
0.5
|
|
C14
|
A:ZAR701
|
1.4
|
21.5
|
0.4
|
|
C14
|
A:ZAR701
|
1.5
|
22.1
|
0.5
|
|
F17
|
A:ZAR701
|
1.8
|
23.9
|
0.5
|
|
O18
|
A:ZAR701
|
2.1
|
21.6
|
0.2
|
|
F16
|
A:ZAR701
|
2.2
|
20.8
|
0.4
|
|
O15
|
A:ZAR701
|
2.3
|
18.9
|
0.5
|
|
O15
|
A:ZAR701
|
2.3
|
19.6
|
0.4
|
|
C12
|
A:ZAR701
|
2.7
|
18.2
|
0.5
|
|
C11
|
A:ZAR701
|
2.8
|
18.8
|
0.5
|
|
C10
|
A:ZAR701
|
2.8
|
22.4
|
0.2
|
|
C9
|
A:ZAR701
|
2.8
|
22.8
|
0.2
|
|
C12
|
A:ZAR701
|
2.8
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
2.8
|
19.6
|
0.4
|
|
SD
|
A:MET357
|
3.2
|
18.2
|
1.0
|
|
CE
|
A:MET357
|
3.4
|
18.6
|
1.0
|
|
CE2
|
A:PHE340
|
3.5
|
11.9
|
1.0
|
|
CZ
|
A:PHE340
|
4.0
|
11.7
|
1.0
|
|
C13
|
A:ZAR701
|
4.1
|
18.1
|
0.5
|
|
C13
|
A:ZAR701
|
4.1
|
19.2
|
0.4
|
|
C10
|
A:ZAR701
|
4.2
|
18.4
|
0.5
|
|
C11
|
A:ZAR701
|
4.2
|
22.3
|
0.2
|
|
C8
|
A:ZAR701
|
4.2
|
23.6
|
0.2
|
|
C10
|
A:ZAR701
|
4.2
|
19.1
|
0.4
|
|
N4
|
A:ZAR701
|
4.4
|
25.0
|
0.2
|
|
CG
|
A:PHE372
|
4.5
|
10.8
|
1.0
|
|
NE2
|
A:GLN369
|
4.5
|
11.0
|
1.0
|
|
CD1
|
A:PHE372
|
4.6
|
12.1
|
1.0
|
|
O
|
A:HOH1102
|
4.6
|
30.0
|
1.0
|
|
CD2
|
A:PHE340
|
4.6
|
10.9
|
1.0
|
|
CB
|
A:PHE372
|
4.6
|
10.1
|
1.0
|
|
O15
|
A:ZAR701
|
4.7
|
22.0
|
0.2
|
|
O18
|
A:ZAR701
|
4.7
|
19.1
|
0.5
|
|
O18
|
A:ZAR701
|
4.8
|
19.6
|
0.4
|
|
O
|
A:HOH1226
|
4.8
|
39.9
|
1.0
|
|
C5
|
A:ZAR701
|
4.8
|
24.5
|
0.2
|
|
CG
|
A:MET357
|
4.9
|
16.0
|
1.0
|
|
CD2
|
A:PHE372
|
4.9
|
11.0
|
1.0
|
|
O
|
A:SER368
|
5.0
|
9.0
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 6 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F701
b:21.9
occ:0.17
|
F17
|
A:ZAR701
|
0.0
|
21.9
|
0.2
|
|
C19
|
A:ZAR701
|
1.2
|
20.4
|
0.4
|
|
C19
|
A:ZAR701
|
1.3
|
20.1
|
0.5
|
|
C14
|
A:ZAR701
|
1.4
|
22.1
|
0.2
|
|
F16
|
A:ZAR701
|
2.2
|
21.6
|
0.2
|
|
O18
|
A:ZAR701
|
2.2
|
19.6
|
0.4
|
|
O15
|
A:ZAR701
|
2.3
|
22.0
|
0.2
|
|
O18
|
A:ZAR701
|
2.3
|
19.1
|
0.5
|
|
OG1
|
A:THR333
|
3.1
|
9.2
|
1.0
|
|
CA
|
A:THR333
|
3.3
|
8.2
|
1.0
|
|
N
|
A:THR333
|
3.3
|
8.2
|
1.0
|
|
C10
|
A:ZAR701
|
3.5
|
19.1
|
0.4
|
|
C11
|
A:ZAR701
|
3.5
|
22.3
|
0.2
|
|
C10
|
A:ZAR701
|
3.5
|
18.4
|
0.5
|
|
C
|
A:TRP332
|
3.5
|
8.5
|
1.0
|
|
O
|
A:TRP332
|
3.7
|
7.9
|
1.0
|
|
CB
|
A:THR333
|
3.7
|
8.2
|
1.0
|
|
OE1
|
A:GLN369
|
3.7
|
9.6
|
1.0
|
|
NE2
|
A:GLN369
|
3.8
|
11.0
|
1.0
|
|
CE1
|
A:TYR329
|
3.8
|
6.9
|
1.0
|
|
CG2
|
A:ILE336
|
4.0
|
8.0
|
1.0
|
|
CD
|
A:GLN369
|
4.0
|
9.6
|
1.0
|
|
CB
|
A:TRP332
|
4.0
|
8.4
|
1.0
|
|
OD1
|
A:ASN321
|
4.1
|
12.1
|
1.0
|
|
C9
|
A:ZAR701
|
4.1
|
19.0
|
0.4
|
|
C12
|
A:ZAR701
|
4.1
|
22.7
|
0.2
|
|
C9
|
A:ZAR701
|
4.2
|
18.1
|
0.5
|
|
CD1
|
A:TYR329
|
4.2
|
6.6
|
1.0
|
|
CB
|
A:ASN321
|
4.3
|
9.5
|
1.0
|
|
O
|
A:TYR329
|
4.4
|
7.9
|
1.0
|
|
CA
|
A:TRP332
|
4.4
|
8.2
|
1.0
|
|
CG2
|
A:THR333
|
4.5
|
8.8
|
1.0
|
|
O15
|
A:ZAR701
|
4.5
|
18.9
|
0.5
|
|
C11
|
A:ZAR701
|
4.6
|
18.8
|
0.5
|
|
C11
|
A:ZAR701
|
4.6
|
19.6
|
0.4
|
|
O15
|
A:ZAR701
|
4.6
|
19.6
|
0.4
|
|
C10
|
A:ZAR701
|
4.6
|
22.4
|
0.2
|
|
C
|
A:THR333
|
4.6
|
8.3
|
1.0
|
|
O18
|
A:ZAR701
|
4.6
|
21.6
|
0.2
|
|
CG
|
A:ASN321
|
4.7
|
11.6
|
1.0
|
|
CB
|
A:ILE336
|
4.7
|
8.0
|
1.0
|
|
O
|
A:THR333
|
5.0
|
8.3
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 7 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F704
b:24.5
occ:0.50
|
F16
|
B:ZAR704
|
0.0
|
24.5
|
0.5
|
|
C14
|
B:ZAR704
|
1.1
|
19.6
|
0.3
|
|
F17
|
B:ZAR704
|
1.1
|
18.5
|
0.3
|
|
C14
|
B:ZAR704
|
1.4
|
22.8
|
0.5
|
|
C19
|
B:ZAR704
|
1.6
|
23.4
|
0.2
|
|
F16
|
B:ZAR704
|
1.9
|
19.1
|
0.3
|
|
O18
|
B:ZAR704
|
2.2
|
22.8
|
0.2
|
|
F17
|
B:ZAR704
|
2.2
|
23.1
|
0.5
|
|
O15
|
B:ZAR704
|
2.3
|
21.4
|
0.5
|
|
O15
|
B:ZAR704
|
2.4
|
19.9
|
0.3
|
|
C9
|
B:ZAR704
|
2.7
|
23.2
|
0.2
|
|
C10
|
B:ZAR704
|
2.8
|
22.9
|
0.2
|
|
SD
|
B:MET357
|
2.9
|
17.2
|
1.0
|
|
C12
|
B:ZAR704
|
2.9
|
20.4
|
0.5
|
|
C11
|
B:ZAR704
|
2.9
|
20.6
|
0.5
|
|
C12
|
B:ZAR704
|
3.0
|
21.2
|
0.3
|
|
C11
|
B:ZAR704
|
3.0
|
20.8
|
0.3
|
|
CE
|
B:MET357
|
3.1
|
17.0
|
1.0
|
|
CE2
|
B:PHE340
|
3.5
|
12.3
|
1.0
|
|
C8
|
B:ZAR704
|
4.0
|
24.0
|
0.2
|
|
CZ
|
B:PHE340
|
4.1
|
11.9
|
1.0
|
|
C11
|
B:ZAR704
|
4.1
|
22.9
|
0.2
|
|
N4
|
B:ZAR704
|
4.2
|
25.0
|
0.2
|
|
C13
|
B:ZAR704
|
4.3
|
20.6
|
0.5
|
|
C13
|
B:ZAR704
|
4.3
|
21.4
|
0.3
|
|
C10
|
B:ZAR704
|
4.3
|
21.1
|
0.5
|
|
C10
|
B:ZAR704
|
4.3
|
21.5
|
0.3
|
|
CD2
|
B:PHE340
|
4.5
|
11.1
|
1.0
|
|
CG
|
B:MET357
|
4.6
|
13.9
|
1.0
|
|
NE2
|
B:GLN369
|
4.6
|
13.3
|
1.0
|
|
O
|
B:HOH2237
|
4.6
|
37.2
|
1.0
|
|
C5
|
B:ZAR704
|
4.7
|
24.5
|
0.2
|
|
CG
|
B:PHE372
|
4.7
|
11.1
|
1.0
|
|
O15
|
B:ZAR704
|
4.7
|
22.1
|
0.2
|
|
CD1
|
B:PHE372
|
4.7
|
12.8
|
1.0
|
|
O
|
B:HOH2131
|
4.8
|
29.4
|
1.0
|
|
CB
|
B:PHE372
|
4.8
|
10.4
|
1.0
|
|
O
|
B:HOH2132
|
4.8
|
34.4
|
1.0
|
|
O18
|
B:ZAR704
|
4.8
|
21.1
|
0.5
|
|
O18
|
B:ZAR704
|
4.9
|
21.7
|
0.3
|
|
Fluorine binding site 8 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 8 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F704
b:19.1
occ:0.28
|
F16
|
B:ZAR704
|
0.0
|
19.1
|
0.3
|
|
F17
|
B:ZAR704
|
1.2
|
23.1
|
0.5
|
|
C14
|
B:ZAR704
|
1.4
|
19.6
|
0.3
|
|
C19
|
B:ZAR704
|
1.4
|
23.4
|
0.2
|
|
C14
|
B:ZAR704
|
1.7
|
22.8
|
0.5
|
|
F16
|
B:ZAR704
|
1.9
|
24.5
|
0.5
|
|
O18
|
B:ZAR704
|
2.0
|
22.8
|
0.2
|
|
F17
|
B:ZAR704
|
2.2
|
18.5
|
0.3
|
|
O15
|
B:ZAR704
|
2.2
|
21.4
|
0.5
|
|
O15
|
B:ZAR704
|
2.3
|
19.9
|
0.3
|
|
O
|
B:HOH2131
|
3.0
|
29.4
|
1.0
|
|
NE2
|
B:GLN369
|
3.0
|
13.3
|
1.0
|
|
SD
|
B:MET357
|
3.3
|
17.2
|
1.0
|
|
C10
|
B:ZAR704
|
3.3
|
22.9
|
0.2
|
|
C11
|
B:ZAR704
|
3.5
|
20.6
|
0.5
|
|
C11
|
B:ZAR704
|
3.5
|
20.8
|
0.3
|
|
CB
|
B:SER368
|
3.8
|
9.3
|
1.0
|
|
O
|
B:SER368
|
3.9
|
8.8
|
1.0
|
|
CD
|
B:GLN369
|
4.0
|
10.2
|
1.0
|
|
C9
|
B:ZAR704
|
4.0
|
23.2
|
0.2
|
|
C
|
B:SER368
|
4.0
|
8.9
|
1.0
|
|
C12
|
B:ZAR704
|
4.2
|
20.4
|
0.5
|
|
C12
|
B:ZAR704
|
4.2
|
21.2
|
0.3
|
|
N
|
B:GLN369
|
4.3
|
8.8
|
1.0
|
|
CE
|
B:MET357
|
4.4
|
17.0
|
1.0
|
|
O15
|
B:ZAR704
|
4.4
|
22.1
|
0.2
|
|
C11
|
B:ZAR704
|
4.4
|
22.9
|
0.2
|
|
CB
|
B:PHE372
|
4.4
|
10.4
|
1.0
|
|
SD
|
B:MET337
|
4.5
|
17.4
|
1.0
|
|
O18
|
B:ZAR704
|
4.5
|
21.1
|
0.5
|
|
C10
|
B:ZAR704
|
4.6
|
21.1
|
0.5
|
|
O18
|
B:ZAR704
|
4.6
|
21.7
|
0.3
|
|
CA
|
B:SER368
|
4.6
|
9.3
|
1.0
|
|
C10
|
B:ZAR704
|
4.6
|
21.5
|
0.3
|
|
CA
|
B:GLN369
|
4.6
|
8.7
|
1.0
|
|
CE2
|
B:PHE340
|
4.6
|
12.3
|
1.0
|
|
OE1
|
B:GLN369
|
4.7
|
12.1
|
1.0
|
|
O
|
B:HOH2132
|
4.7
|
34.4
|
1.0
|
|
CG
|
B:PHE372
|
4.7
|
11.1
|
1.0
|
|
CG
|
B:GLN369
|
4.7
|
9.7
|
1.0
|
|
CG
|
B:MET357
|
4.8
|
13.9
|
1.0
|
|
CD2
|
B:PHE372
|
4.8
|
12.7
|
1.0
|
|
OG
|
B:SER368
|
4.9
|
10.9
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 9 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F704
b:21.6
occ:0.22
|
F16
|
B:ZAR704
|
0.0
|
21.6
|
0.2
|
|
C14
|
B:ZAR704
|
1.4
|
22.1
|
0.2
|
|
C19
|
B:ZAR704
|
1.8
|
22.3
|
0.5
|
|
C19
|
B:ZAR704
|
1.9
|
22.5
|
0.3
|
|
O18
|
B:ZAR704
|
2.2
|
21.1
|
0.5
|
|
O18
|
B:ZAR704
|
2.2
|
21.7
|
0.3
|
|
F17
|
B:ZAR704
|
2.2
|
21.8
|
0.2
|
|
O15
|
B:ZAR704
|
2.3
|
22.1
|
0.2
|
|
C10
|
B:ZAR704
|
3.0
|
21.5
|
0.3
|
|
C10
|
B:ZAR704
|
3.1
|
21.1
|
0.5
|
|
C11
|
B:ZAR704
|
3.2
|
22.9
|
0.2
|
|
CE2
|
B:PHE372
|
3.4
|
12.5
|
1.0
|
|
CB
|
B:ASN321
|
3.4
|
8.8
|
1.0
|
|
C9
|
B:ZAR704
|
3.5
|
21.6
|
0.3
|
|
CG
|
B:PRO322
|
3.5
|
8.6
|
1.0
|
|
C12
|
B:ZAR704
|
3.5
|
23.4
|
0.2
|
|
C9
|
B:ZAR704
|
3.6
|
20.7
|
0.5
|
|
OD1
|
B:ASN321
|
3.6
|
11.9
|
1.0
|
|
CE1
|
B:TYR329
|
3.6
|
8.5
|
1.0
|
|
CD
|
B:PRO322
|
3.6
|
8.7
|
1.0
|
|
OE1
|
B:GLN369
|
3.6
|
12.1
|
1.0
|
|
CG
|
B:ASN321
|
4.0
|
10.2
|
1.0
|
|
CD2
|
B:PHE372
|
4.0
|
12.7
|
1.0
|
|
O
|
B:HOH2014
|
4.1
|
18.5
|
1.0
|
|
C11
|
B:ZAR704
|
4.1
|
20.8
|
0.3
|
|
CD1
|
B:TYR329
|
4.2
|
8.4
|
1.0
|
|
C11
|
B:ZAR704
|
4.2
|
20.6
|
0.5
|
|
N
|
B:PRO322
|
4.2
|
8.6
|
1.0
|
|
C10
|
B:ZAR704
|
4.4
|
22.9
|
0.2
|
|
NE2
|
B:GLN369
|
4.4
|
13.3
|
1.0
|
|
CD
|
B:GLN369
|
4.4
|
10.2
|
1.0
|
|
O15
|
B:ZAR704
|
4.4
|
19.9
|
0.3
|
|
CZ
|
B:PHE372
|
4.4
|
13.1
|
1.0
|
|
O15
|
B:ZAR704
|
4.5
|
21.4
|
0.5
|
|
CA
|
B:ASN321
|
4.5
|
9.2
|
1.0
|
|
OG1
|
B:THR333
|
4.6
|
9.2
|
1.0
|
|
CZ
|
B:TYR329
|
4.6
|
8.2
|
1.0
|
|
C
|
B:ASN321
|
4.6
|
8.9
|
1.0
|
|
O18
|
B:ZAR704
|
4.7
|
22.8
|
0.2
|
|
OH
|
B:TYR329
|
4.7
|
9.8
|
1.0
|
|
C8
|
B:ZAR704
|
4.8
|
21.4
|
0.3
|
|
CB
|
B:PRO322
|
4.8
|
8.6
|
1.0
|
|
C13
|
B:ZAR704
|
4.9
|
23.6
|
0.2
|
|
C8
|
B:ZAR704
|
4.9
|
20.0
|
0.5
|
|
CA
|
B:PRO322
|
5.0
|
8.4
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 1xor
Go back to
Fluorine Binding Sites List in 1xor
Fluorine binding site 10 out
of 12 in the Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Catalytic Domain of Human Phosphodiesterase 4D in Complex with Zardaverine within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F704
b:23.1
occ:0.50
|
F17
|
B:ZAR704
|
0.0
|
23.1
|
0.5
|
|
C19
|
B:ZAR704
|
1.0
|
23.4
|
0.2
|
|
F16
|
B:ZAR704
|
1.2
|
19.1
|
0.3
|
|
C14
|
B:ZAR704
|
1.4
|
22.8
|
0.5
|
|
C14
|
B:ZAR704
|
1.6
|
19.6
|
0.3
|
|
F17
|
B:ZAR704
|
1.8
|
18.5
|
0.3
|
|
O15
|
B:ZAR704
|
2.2
|
19.9
|
0.3
|
|
F16
|
B:ZAR704
|
2.2
|
24.5
|
0.5
|
|
O15
|
B:ZAR704
|
2.2
|
21.4
|
0.5
|
|
O18
|
B:ZAR704
|
2.3
|
22.8
|
0.2
|
|
O
|
B:SER368
|
3.2
|
8.8
|
1.0
|
|
CB
|
B:PHE372
|
3.2
|
10.4
|
1.0
|
|
NE2
|
B:GLN369
|
3.2
|
13.3
|
1.0
|
|
C10
|
B:ZAR704
|
3.4
|
22.9
|
0.2
|
|
C11
|
B:ZAR704
|
3.5
|
20.8
|
0.3
|
|
C11
|
B:ZAR704
|
3.5
|
20.6
|
0.5
|
|
CG
|
B:PHE372
|
3.5
|
11.1
|
1.0
|
|
C
|
B:SER368
|
3.6
|
8.9
|
1.0
|
|
SD
|
B:MET357
|
3.7
|
17.2
|
1.0
|
|
O
|
B:HOH2131
|
3.9
|
29.4
|
1.0
|
|
CD2
|
B:PHE372
|
3.9
|
12.7
|
1.0
|
|
CD
|
B:GLN369
|
3.9
|
10.2
|
1.0
|
|
C9
|
B:ZAR704
|
4.0
|
23.2
|
0.2
|
|
O
|
B:HOH2132
|
4.0
|
34.4
|
1.0
|
|
N
|
B:GLN369
|
4.0
|
8.8
|
1.0
|
|
C12
|
B:ZAR704
|
4.1
|
21.2
|
0.3
|
|
CA
|
B:GLN369
|
4.1
|
8.7
|
1.0
|
|
CB
|
B:SER368
|
4.1
|
9.3
|
1.0
|
|
C12
|
B:ZAR704
|
4.2
|
20.4
|
0.5
|
|
CD1
|
B:PHE372
|
4.2
|
12.8
|
1.0
|
|
OE1
|
B:GLN369
|
4.3
|
12.1
|
1.0
|
|
C11
|
B:ZAR704
|
4.4
|
22.9
|
0.2
|
|
O15
|
B:ZAR704
|
4.4
|
22.1
|
0.2
|
|
CA
|
B:SER368
|
4.5
|
9.3
|
1.0
|
|
CA
|
B:PHE372
|
4.5
|
9.8
|
1.0
|
|
O18
|
B:ZAR704
|
4.5
|
21.1
|
0.5
|
|
O
|
B:HOH2237
|
4.5
|
37.2
|
1.0
|
|
C10
|
B:ZAR704
|
4.5
|
21.5
|
0.3
|
|
C10
|
B:ZAR704
|
4.6
|
21.1
|
0.5
|
|
O18
|
B:ZAR704
|
4.6
|
21.7
|
0.3
|
|
CE
|
B:MET357
|
4.7
|
17.0
|
1.0
|
|
CG
|
B:GLN369
|
4.7
|
9.7
|
1.0
|
|
N
|
B:PHE372
|
4.8
|
9.5
|
1.0
|
|
CE2
|
B:PHE372
|
4.8
|
12.5
|
1.0
|
|
Reference:
G.L.Card,
B.P.England,
Y.Suzuki,
D.Fong,
B.Powell,
B.Lee,
C.Luu,
M.Tabrizizad,
S.Gillette,
P.N.Ibrahim,
D.R.Artis,
G.Bollag,
M.V.Milburn,
S.-H.Kim,
J.Schlessinger,
K.Y.J.Zhang.
Structural Basis For the Activity of Drugs That Inhibit Phosphodiesterases. Structure V. 12 2233 2004.
ISSN: ISSN 0969-2126
PubMed: 15576036
DOI: 10.1016/J.STR.2004.10.004
Page generated: Sun Dec 13 11:34:01 2020
|
