Fluorine in PDB 3v9b: Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide:
3.1.4.17;
Protein crystallography data
The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide, PDB code: 3v9b
was solved by
H.T.Kim,
H.J.Chang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
35.41 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.587,
110.293,
161.607,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.6 /
23.6
|
Other elements in 3v9b:
The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
(pdb code 3v9b). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide, PDB code: 3v9b:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 1 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:27.5
occ:1.00
|
F09
|
A:IHM1
|
0.0
|
27.5
|
1.0
|
C08
|
A:IHM1
|
1.4
|
27.2
|
1.0
|
F10
|
A:IHM1
|
2.2
|
26.2
|
1.0
|
O07
|
A:IHM1
|
2.3
|
25.9
|
1.0
|
C01
|
A:IHM1
|
3.1
|
25.8
|
1.0
|
N
|
A:THR333
|
3.1
|
22.3
|
1.0
|
C
|
A:TRP332
|
3.1
|
23.0
|
1.0
|
C02
|
A:IHM1
|
3.2
|
25.3
|
1.0
|
O
|
A:TRP332
|
3.3
|
22.4
|
1.0
|
CA
|
A:THR333
|
3.3
|
23.7
|
1.0
|
CB
|
A:TRP332
|
3.4
|
20.1
|
1.0
|
OD1
|
A:ASN321
|
3.6
|
20.4
|
1.0
|
OG1
|
A:THR333
|
3.7
|
23.8
|
1.0
|
CG2
|
A:ILE336
|
3.8
|
26.0
|
1.0
|
CA
|
A:TRP332
|
3.9
|
22.4
|
1.0
|
CB
|
A:ASN321
|
4.1
|
18.9
|
1.0
|
CB
|
A:THR333
|
4.1
|
23.8
|
1.0
|
CB
|
A:ILE336
|
4.2
|
24.3
|
1.0
|
CG
|
A:ASN321
|
4.2
|
21.0
|
1.0
|
CE1
|
A:TYR159
|
4.3
|
18.8
|
1.0
|
C06
|
A:IHM1
|
4.4
|
26.0
|
1.0
|
O
|
A:TYR329
|
4.5
|
24.7
|
1.0
|
C
|
A:THR333
|
4.5
|
25.1
|
1.0
|
C03
|
A:IHM1
|
4.6
|
25.2
|
1.0
|
CE1
|
A:TYR329
|
4.6
|
20.6
|
1.0
|
CG
|
A:TRP332
|
4.7
|
20.6
|
1.0
|
CD1
|
A:TYR329
|
4.7
|
22.1
|
1.0
|
NE2
|
A:GLN369
|
4.8
|
19.8
|
1.0
|
O11
|
A:IHM1
|
4.9
|
26.0
|
1.0
|
O
|
A:THR333
|
4.9
|
24.4
|
1.0
|
OE1
|
A:GLN369
|
4.9
|
22.7
|
1.0
|
N
|
A:TRP332
|
5.0
|
21.9
|
1.0
|
CD1
|
A:TYR159
|
5.0
|
18.4
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 2 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1
b:26.2
occ:1.00
|
F10
|
A:IHM1
|
0.0
|
26.2
|
1.0
|
C08
|
A:IHM1
|
1.4
|
27.2
|
1.0
|
F09
|
A:IHM1
|
2.2
|
27.5
|
1.0
|
O07
|
A:IHM1
|
2.3
|
25.9
|
1.0
|
C01
|
A:IHM1
|
3.0
|
25.8
|
1.0
|
C02
|
A:IHM1
|
3.1
|
25.3
|
1.0
|
CB
|
A:ASN321
|
3.2
|
18.9
|
1.0
|
CE1
|
A:TYR329
|
3.2
|
20.6
|
1.0
|
CG
|
A:PRO322
|
3.6
|
22.9
|
1.0
|
CD
|
A:PRO322
|
3.7
|
22.0
|
1.0
|
CD1
|
A:TYR329
|
3.7
|
22.1
|
1.0
|
OE1
|
A:GLN369
|
3.7
|
22.7
|
1.0
|
OD1
|
A:ASN321
|
3.8
|
20.4
|
1.0
|
CG
|
A:ASN321
|
4.0
|
21.0
|
1.0
|
CE2
|
A:PHE372
|
4.0
|
28.9
|
1.0
|
OG1
|
A:THR333
|
4.1
|
23.8
|
1.0
|
N
|
A:PRO322
|
4.2
|
21.4
|
1.0
|
C06
|
A:IHM1
|
4.3
|
26.0
|
1.0
|
CZ
|
A:TYR329
|
4.4
|
22.6
|
1.0
|
CA
|
A:ASN321
|
4.4
|
18.9
|
1.0
|
C
|
A:ASN321
|
4.4
|
20.9
|
1.0
|
O
|
A:HOH478
|
4.4
|
24.7
|
1.0
|
C03
|
A:IHM1
|
4.4
|
25.2
|
1.0
|
CD
|
A:GLN369
|
4.5
|
24.2
|
1.0
|
CD2
|
A:PHE372
|
4.5
|
27.3
|
1.0
|
CB
|
A:TRP332
|
4.6
|
20.1
|
1.0
|
NE2
|
A:GLN369
|
4.6
|
19.8
|
1.0
|
OH
|
A:TYR329
|
4.6
|
21.1
|
1.0
|
N
|
A:THR333
|
4.7
|
22.3
|
1.0
|
O11
|
A:IHM1
|
4.8
|
26.0
|
1.0
|
CB
|
A:PRO322
|
4.8
|
22.7
|
1.0
|
CA
|
A:PRO322
|
4.9
|
22.2
|
1.0
|
O
|
A:TYR329
|
4.9
|
24.7
|
1.0
|
CA
|
A:THR333
|
4.9
|
23.7
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 3 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:21.7
occ:1.00
|
F09
|
B:IHM1
|
0.0
|
21.7
|
1.0
|
C08
|
B:IHM1
|
1.4
|
21.6
|
1.0
|
F10
|
B:IHM1
|
2.2
|
20.7
|
1.0
|
O07
|
B:IHM1
|
2.3
|
21.5
|
1.0
|
C01
|
B:IHM1
|
3.0
|
22.9
|
1.0
|
C
|
B:TRP332
|
3.2
|
23.2
|
1.0
|
C02
|
B:IHM1
|
3.2
|
22.2
|
1.0
|
O
|
B:TRP332
|
3.2
|
23.1
|
1.0
|
N
|
B:THR333
|
3.2
|
23.2
|
1.0
|
CA
|
B:THR333
|
3.4
|
22.2
|
1.0
|
CB
|
B:TRP332
|
3.5
|
24.6
|
1.0
|
OD1
|
B:ASN321
|
3.5
|
26.0
|
1.0
|
CG2
|
B:ILE336
|
3.7
|
21.8
|
1.0
|
OG1
|
B:THR333
|
3.7
|
21.4
|
1.0
|
CA
|
B:TRP332
|
4.0
|
24.0
|
1.0
|
CB
|
B:ILE336
|
4.1
|
23.0
|
1.0
|
CB
|
B:ASN321
|
4.1
|
21.9
|
1.0
|
CE1
|
B:TYR159
|
4.2
|
20.5
|
1.0
|
CB
|
B:THR333
|
4.2
|
22.2
|
1.0
|
CG
|
B:ASN321
|
4.2
|
23.4
|
1.0
|
C06
|
B:IHM1
|
4.4
|
24.1
|
1.0
|
C03
|
B:IHM1
|
4.5
|
22.6
|
1.0
|
C
|
B:THR333
|
4.6
|
23.3
|
1.0
|
O
|
B:TYR329
|
4.6
|
25.2
|
1.0
|
CE1
|
B:TYR329
|
4.7
|
20.9
|
1.0
|
CD1
|
B:TYR159
|
4.8
|
20.9
|
1.0
|
CG
|
B:TRP332
|
4.8
|
26.1
|
1.0
|
OE1
|
B:GLN369
|
4.8
|
22.0
|
1.0
|
CD1
|
B:TYR329
|
4.8
|
23.1
|
1.0
|
O11
|
B:IHM1
|
4.8
|
26.6
|
1.0
|
NE2
|
B:GLN369
|
4.9
|
18.2
|
1.0
|
O
|
B:THR333
|
4.9
|
22.4
|
1.0
|
CG1
|
B:ILE336
|
5.0
|
24.9
|
1.0
|
CZ
|
B:TYR159
|
5.0
|
19.3
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 4 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F1
b:20.7
occ:1.00
|
F10
|
B:IHM1
|
0.0
|
20.7
|
1.0
|
C08
|
B:IHM1
|
1.4
|
21.6
|
1.0
|
F09
|
B:IHM1
|
2.2
|
21.7
|
1.0
|
O07
|
B:IHM1
|
2.3
|
21.5
|
1.0
|
C01
|
B:IHM1
|
2.9
|
22.9
|
1.0
|
C02
|
B:IHM1
|
3.1
|
22.2
|
1.0
|
CB
|
B:ASN321
|
3.2
|
21.9
|
1.0
|
CE1
|
B:TYR329
|
3.3
|
20.9
|
1.0
|
OE1
|
B:GLN369
|
3.6
|
22.0
|
1.0
|
CG
|
B:PRO322
|
3.6
|
20.6
|
1.0
|
CD
|
B:PRO322
|
3.7
|
21.3
|
1.0
|
OD1
|
B:ASN321
|
3.8
|
26.0
|
1.0
|
CD1
|
B:TYR329
|
3.8
|
23.1
|
1.0
|
CE2
|
B:PHE372
|
4.0
|
19.3
|
1.0
|
CG
|
B:ASN321
|
4.0
|
23.4
|
1.0
|
OG1
|
B:THR333
|
4.0
|
21.4
|
1.0
|
N
|
B:PRO322
|
4.2
|
21.0
|
1.0
|
C06
|
B:IHM1
|
4.2
|
24.1
|
1.0
|
O
|
B:HOH45
|
4.3
|
19.9
|
1.0
|
C03
|
B:IHM1
|
4.4
|
22.6
|
1.0
|
CA
|
B:ASN321
|
4.4
|
21.1
|
1.0
|
CD
|
B:GLN369
|
4.5
|
20.0
|
1.0
|
CZ
|
B:TYR329
|
4.5
|
22.8
|
1.0
|
CD2
|
B:PHE372
|
4.5
|
18.2
|
1.0
|
C
|
B:ASN321
|
4.5
|
21.8
|
1.0
|
NE2
|
B:GLN369
|
4.6
|
18.2
|
1.0
|
CB
|
B:TRP332
|
4.7
|
24.6
|
1.0
|
OH
|
B:TYR329
|
4.7
|
19.9
|
1.0
|
O11
|
B:IHM1
|
4.8
|
26.6
|
1.0
|
CB
|
B:PRO322
|
4.8
|
21.3
|
1.0
|
N
|
B:THR333
|
4.8
|
23.2
|
1.0
|
CA
|
B:PRO322
|
4.8
|
21.7
|
1.0
|
CA
|
B:THR333
|
4.9
|
22.2
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 5 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1
b:30.3
occ:1.00
|
F09
|
C:IHM1
|
0.0
|
30.3
|
1.0
|
C08
|
C:IHM1
|
1.4
|
26.7
|
1.0
|
F10
|
C:IHM1
|
2.2
|
26.1
|
1.0
|
O07
|
C:IHM1
|
2.3
|
26.1
|
1.0
|
C
|
C:TRP332
|
2.9
|
24.2
|
1.0
|
O
|
C:TRP332
|
3.0
|
25.1
|
1.0
|
C01
|
C:IHM1
|
3.0
|
27.5
|
1.0
|
N
|
C:THR333
|
3.1
|
23.7
|
1.0
|
C02
|
C:IHM1
|
3.2
|
26.8
|
1.0
|
CB
|
C:TRP332
|
3.3
|
21.1
|
1.0
|
CA
|
C:THR333
|
3.3
|
23.8
|
1.0
|
OD1
|
C:ASN321
|
3.5
|
21.4
|
1.0
|
CA
|
C:TRP332
|
3.7
|
23.5
|
1.0
|
OG1
|
C:THR333
|
3.7
|
20.6
|
1.0
|
CG2
|
C:ILE336
|
3.8
|
20.6
|
1.0
|
CB
|
C:ASN321
|
4.1
|
20.0
|
1.0
|
CB
|
C:ILE336
|
4.1
|
21.2
|
1.0
|
CG
|
C:ASN321
|
4.1
|
22.6
|
1.0
|
CE1
|
C:TYR159
|
4.2
|
18.2
|
1.0
|
CB
|
C:THR333
|
4.2
|
23.0
|
1.0
|
C06
|
C:IHM1
|
4.4
|
27.6
|
1.0
|
C
|
C:THR333
|
4.5
|
25.3
|
1.0
|
O
|
C:TYR329
|
4.5
|
23.9
|
1.0
|
C03
|
C:IHM1
|
4.6
|
27.6
|
1.0
|
CE1
|
C:TYR329
|
4.6
|
27.6
|
1.0
|
CG
|
C:TRP332
|
4.6
|
22.1
|
1.0
|
CD1
|
C:TYR329
|
4.7
|
28.5
|
1.0
|
CD1
|
C:TYR159
|
4.8
|
16.0
|
1.0
|
OE1
|
C:GLN369
|
4.8
|
24.6
|
1.0
|
NE2
|
C:GLN369
|
4.8
|
22.1
|
1.0
|
O11
|
C:IHM1
|
4.8
|
27.1
|
1.0
|
N
|
C:TRP332
|
4.9
|
23.3
|
1.0
|
O
|
C:THR333
|
4.9
|
26.7
|
1.0
|
CZ
|
C:TYR159
|
5.0
|
16.9
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 6 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 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 the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1
b:26.1
occ:1.00
|
F10
|
C:IHM1
|
0.0
|
26.1
|
1.0
|
C08
|
C:IHM1
|
1.4
|
26.7
|
1.0
|
F09
|
C:IHM1
|
2.2
|
30.3
|
1.0
|
O07
|
C:IHM1
|
2.3
|
26.1
|
1.0
|
C01
|
C:IHM1
|
3.0
|
27.5
|
1.0
|
C02
|
C:IHM1
|
3.1
|
26.8
|
1.0
|
CB
|
C:ASN321
|
3.1
|
20.0
|
1.0
|
CE1
|
C:TYR329
|
3.2
|
27.6
|
1.0
|
OE1
|
C:GLN369
|
3.6
|
24.6
|
1.0
|
OD1
|
C:ASN321
|
3.7
|
21.4
|
1.0
|
CG
|
C:PRO322
|
3.7
|
24.6
|
1.0
|
CD1
|
C:TYR329
|
3.7
|
28.5
|
1.0
|
CD
|
C:PRO322
|
3.8
|
22.6
|
1.0
|
CG
|
C:ASN321
|
3.9
|
22.6
|
1.0
|
OG1
|
C:THR333
|
4.0
|
20.6
|
1.0
|
CE2
|
C:PHE372
|
4.1
|
22.7
|
1.0
|
N
|
C:PRO322
|
4.2
|
23.8
|
1.0
|
O
|
C:HOH32
|
4.2
|
23.9
|
1.0
|
C06
|
C:IHM1
|
4.3
|
27.6
|
1.0
|
CZ
|
C:TYR329
|
4.4
|
28.4
|
1.0
|
CA
|
C:ASN321
|
4.4
|
20.8
|
1.0
|
CD
|
C:GLN369
|
4.4
|
25.7
|
1.0
|
C
|
C:ASN321
|
4.4
|
22.9
|
1.0
|
C03
|
C:IHM1
|
4.4
|
27.6
|
1.0
|
CB
|
C:TRP332
|
4.5
|
21.1
|
1.0
|
NE2
|
C:GLN369
|
4.5
|
22.1
|
1.0
|
CD2
|
C:PHE372
|
4.6
|
21.7
|
1.0
|
OH
|
C:TYR329
|
4.6
|
27.9
|
1.0
|
N
|
C:THR333
|
4.7
|
23.7
|
1.0
|
O11
|
C:IHM1
|
4.8
|
27.1
|
1.0
|
CA
|
C:THR333
|
4.9
|
23.8
|
1.0
|
CA
|
C:PRO322
|
4.9
|
24.2
|
1.0
|
C
|
C:TRP332
|
4.9
|
24.2
|
1.0
|
CB
|
C:PRO322
|
4.9
|
23.6
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 7 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1
b:23.0
occ:1.00
|
F09
|
D:IHM1
|
0.0
|
23.0
|
1.0
|
C08
|
D:IHM1
|
1.4
|
20.8
|
1.0
|
F10
|
D:IHM1
|
2.2
|
20.9
|
1.0
|
O07
|
D:IHM1
|
2.3
|
22.1
|
1.0
|
C01
|
D:IHM1
|
3.0
|
20.6
|
1.0
|
C
|
D:TRP332
|
3.0
|
18.8
|
1.0
|
N
|
D:THR333
|
3.1
|
19.9
|
1.0
|
C02
|
D:IHM1
|
3.2
|
19.5
|
1.0
|
O
|
D:TRP332
|
3.2
|
18.7
|
1.0
|
CA
|
D:THR333
|
3.3
|
19.8
|
1.0
|
CB
|
D:TRP332
|
3.4
|
17.5
|
1.0
|
CG2
|
D:ILE336
|
3.6
|
19.5
|
1.0
|
OD1
|
D:ASN321
|
3.7
|
17.5
|
1.0
|
OG1
|
D:THR333
|
3.8
|
19.2
|
1.0
|
CA
|
D:TRP332
|
3.8
|
19.0
|
1.0
|
CB
|
D:ILE336
|
4.1
|
21.5
|
1.0
|
CB
|
D:THR333
|
4.2
|
20.6
|
1.0
|
CB
|
D:ASN321
|
4.2
|
14.4
|
1.0
|
CE1
|
D:TYR159
|
4.3
|
16.4
|
1.0
|
CG
|
D:ASN321
|
4.3
|
17.5
|
1.0
|
C06
|
D:IHM1
|
4.4
|
22.0
|
1.0
|
C
|
D:THR333
|
4.5
|
21.1
|
1.0
|
O
|
D:TYR329
|
4.5
|
18.2
|
1.0
|
C03
|
D:IHM1
|
4.5
|
18.4
|
1.0
|
CE1
|
D:TYR329
|
4.6
|
19.5
|
1.0
|
CG
|
D:TRP332
|
4.7
|
17.4
|
1.0
|
OE1
|
D:GLN369
|
4.7
|
21.0
|
1.0
|
CD1
|
D:TYR329
|
4.8
|
17.3
|
1.0
|
NE2
|
D:GLN369
|
4.8
|
19.3
|
1.0
|
O11
|
D:IHM1
|
4.8
|
23.6
|
1.0
|
CD1
|
D:TYR159
|
4.8
|
17.5
|
1.0
|
O
|
D:THR333
|
4.9
|
22.2
|
1.0
|
N
|
D:TRP332
|
4.9
|
18.2
|
1.0
|
CG2
|
D:THR333
|
5.0
|
17.8
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 3v9b
Go back to
Fluorine Binding Sites List in 3v9b
Fluorine binding site 8 out
of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide
 Mono view
 Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F1
b:20.9
occ:1.00
|
F10
|
D:IHM1
|
0.0
|
20.9
|
1.0
|
C08
|
D:IHM1
|
1.4
|
20.8
|
1.0
|
F09
|
D:IHM1
|
2.2
|
23.0
|
1.0
|
O07
|
D:IHM1
|
2.2
|
22.1
|
1.0
|
C01
|
D:IHM1
|
2.9
|
20.6
|
1.0
|
C02
|
D:IHM1
|
3.1
|
19.5
|
1.0
|
CB
|
D:ASN321
|
3.2
|
14.4
|
1.0
|
CE1
|
D:TYR329
|
3.2
|
19.5
|
1.0
|
CG
|
D:PRO322
|
3.5
|
18.3
|
1.0
|
CD
|
D:PRO322
|
3.6
|
16.3
|
1.0
|
OE1
|
D:GLN369
|
3.7
|
21.0
|
1.0
|
CD1
|
D:TYR329
|
3.7
|
17.3
|
1.0
|
OD1
|
D:ASN321
|
3.8
|
17.5
|
1.0
|
CG
|
D:ASN321
|
4.0
|
17.5
|
1.0
|
N
|
D:PRO322
|
4.1
|
16.6
|
1.0
|
OG1
|
D:THR333
|
4.2
|
19.2
|
1.0
|
C06
|
D:IHM1
|
4.2
|
22.0
|
1.0
|
CE2
|
D:PHE372
|
4.3
|
21.8
|
1.0
|
O
|
D:HOH456
|
4.4
|
21.0
|
1.0
|
CZ
|
D:TYR329
|
4.4
|
17.6
|
1.0
|
CA
|
D:ASN321
|
4.4
|
15.1
|
1.0
|
C
|
D:ASN321
|
4.4
|
15.4
|
1.0
|
C03
|
D:IHM1
|
4.5
|
18.4
|
1.0
|
CB
|
D:TRP332
|
4.5
|
17.5
|
1.0
|
CD
|
D:GLN369
|
4.5
|
20.5
|
1.0
|
O11
|
D:IHM1
|
4.7
|
23.6
|
1.0
|
NE2
|
D:GLN369
|
4.7
|
19.3
|
1.0
|
N
|
D:THR333
|
4.7
|
19.9
|
1.0
|
CD2
|
D:PHE372
|
4.7
|
19.8
|
1.0
|
OH
|
D:TYR329
|
4.7
|
16.3
|
1.0
|
CB
|
D:PRO322
|
4.8
|
17.8
|
1.0
|
CA
|
D:PRO322
|
4.8
|
17.5
|
1.0
|
O
|
D:TYR329
|
4.9
|
18.2
|
1.0
|
CA
|
D:THR333
|
4.9
|
19.8
|
1.0
|
C
|
D:TRP332
|
5.0
|
18.8
|
1.0
|
|
Reference:
C.M.Park,
D.J.Jeon.
Stereoselective Synthesis of Novel Pyrazole Derivatives Using Tert-Butansulfonamide As A Chiral Auxiliary Org.Biomol.Chem. V. 10 2613 2012.
ISSN: ISSN 1477-0520
PubMed: 22371117
DOI: 10.1039/C2OB06495B
Page generated: Wed Jul 31 23:14:33 2024
|