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Fluorine in PDB 5tkb: Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound, PDB code: 5tkb was solved by J.S.Sack, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.62 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.000, 112.700, 159.880, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 20.9

Other elements in 5tkb:

The structure of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound (pdb code 5tkb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 16 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound, PDB code: 5tkb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 16 in 5tkb

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Fluorine binding site 1 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F807

b:58.7
occ:1.00
 F3 A:7DJ807 0.0 58.7 1.0
C13 A:7DJ807 1.3 56.9 1.0
C14 A:7DJ807 2.3 57.4 1.0
C12 A:7DJ807 2.4 55.3 1.0
F2 A:7DJ807 2.7 57.2 1.0
N5 A:7DJ807 2.8 51.0 1.0
C1 A:7DJ807 3.1 49.3 1.0
N A:7DJ807 3.1 48.6 1.0
CD1 A:ILE502 3.2 35.5 1.0
C17 A:7DJ807 3.6 57.0 1.0
C15 A:7DJ807 3.6 57.3 1.0
CG1 A:ILE502 3.6 31.0 1.0
CE1 A:HIS326 3.7 25.5 1.0
CZ A:PHE506 3.8 32.3 1.0
NE2 A:HIS326 4.0 25.9 1.0
CE1 A:PHE506 4.0 32.4 1.0
C16 A:7DJ807 4.1 57.1 1.0
N1 A:7DJ807 4.1 48.6 1.0
O2 A:7DJ807 4.2 62.6 1.0
C A:7DJ807 4.2 48.2 1.0
N4 A:7DJ807 4.4 53.3 1.0
F A:7DJ807 4.7 56.2 1.0
CE1 A:TYR325 4.8 23.9 1.0
O A:HOH974 4.8 34.0 1.0
ND1 A:HIS326 4.8 26.3 1.0
O A:HOH1024 4.8 48.8 1.0
C6 A:7DJ807 4.9 48.4 1.0
CE2 A:PHE506 4.9 34.3 1.0
CD1 A:TYR325 4.9 25.9 1.0
O A:HOH919 5.0 30.8 1.0
C2 A:7DJ807 5.0 47.8 1.0
CB A:ILE502 5.0 31.2 1.0

Fluorine binding site 2 out of 16 in 5tkb

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Fluorine binding site 2 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F807

b:57.2
occ:1.00
 F2 A:7DJ807 0.0 57.2 1.0
C14 A:7DJ807 1.4 57.4 1.0
C13 A:7DJ807 2.4 56.9 1.0
C15 A:7DJ807 2.4 57.3 1.0
F3 A:7DJ807 2.7 58.7 1.0
O A:HOH1024 2.8 48.8 1.0
O2 A:7DJ807 3.3 62.6 1.0
O A:HOH958 3.3 27.3 1.0
C16 A:7DJ807 3.6 57.1 1.0
C12 A:7DJ807 3.6 55.3 1.0
CE1 A:HIS326 3.8 25.5 1.0
C17 A:7DJ807 4.1 57.0 1.0
NE2 A:HIS326 4.1 25.9 1.0
O A:HOH987 4.3 35.1 1.0
O A:HOH918 4.5 41.5 1.0
CE1 A:PHE506 4.6 32.4 1.0
C9 A:7DJ807 4.7 60.4 1.0
F1 A:7DJ807 4.7 56.3 1.0
CZ A:PHE506 4.8 32.3 1.0
N5 A:7DJ807 4.8 51.0 1.0
ND1 A:HIS326 5.0 26.3 1.0
O A:HOH911 5.0 47.3 1.0

Fluorine binding site 3 out of 16 in 5tkb

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Fluorine binding site 3 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F807

b:56.3
occ:1.00
 F1 A:7DJ807 0.0 56.3 1.0
C16 A:7DJ807 1.4 57.1 1.0
C17 A:7DJ807 2.3 57.0 1.0
C15 A:7DJ807 2.4 57.3 1.0
F A:7DJ807 2.7 56.2 1.0
CG A:MET439 3.4 43.9 1.0
O A:HOH910 3.5 32.1 1.0
O A:THR437 3.5 31.9 1.0
C14 A:7DJ807 3.6 57.4 1.0
O A:HOH963 3.6 29.3 1.0
C12 A:7DJ807 3.6 55.3 1.0
OD2 A:ASP484 3.7 36.7 1.0
O A:HOH901 3.8 32.5 1.0
O A:HOH974 3.9 34.0 1.0
SD A:MET439 3.9 50.6 1.0
C13 A:7DJ807 4.1 56.9 1.0
O A:HOH987 4.2 35.1 1.0
CG A:ASP484 4.5 32.0 1.0
CB A:MET439 4.6 38.1 1.0
F2 A:7DJ807 4.7 57.2 1.0
MG A:MG802 4.7 25.2 1.0
C A:THR437 4.8 31.9 1.0
N A:MET439 4.8 33.4 1.0
CD2 A:LEU485 4.8 36.4 1.0
N5 A:7DJ807 4.8 51.0 1.0
O A:HOH919 4.8 30.8 1.0

Fluorine binding site 4 out of 16 in 5tkb

Go back to Fluorine Binding Sites List in 5tkb
Fluorine binding site 4 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F807

b:56.2
occ:1.00
 F A:7DJ807 0.0 56.2 1.0
C17 A:7DJ807 1.3 57.0 1.0
C16 A:7DJ807 2.3 57.1 1.0
C12 A:7DJ807 2.4 55.3 1.0
F1 A:7DJ807 2.7 56.3 1.0
O A:HOH919 2.8 30.8 1.0
N5 A:7DJ807 2.8 51.0 1.0
CD2 A:LEU485 3.0 36.4 1.0
O A:HOH974 3.6 34.0 1.0
C13 A:7DJ807 3.6 56.9 1.0
C15 A:7DJ807 3.6 57.3 1.0
O A:ASP484 3.8 30.1 1.0
C1 A:7DJ807 3.9 49.3 1.0
CG A:LEU485 4.0 34.5 1.0
C14 A:7DJ807 4.1 57.4 1.0
OD2 A:ASP484 4.1 36.7 1.0
CG A:ASP484 4.2 32.0 1.0
N A:7DJ807 4.3 48.6 1.0
C A:ASP484 4.3 32.4 1.0
OD1 A:ASP484 4.4 30.7 1.0
O A:HOH910 4.6 32.1 1.0
F3 A:7DJ807 4.7 58.7 1.0
N A:LEU485 4.8 29.8 1.0
SD A:MET439 4.8 50.6 1.0
CA A:LEU485 4.8 29.3 1.0
CB A:ASP484 4.8 28.3 1.0
CZ A:PHE538 4.8 37.1 1.0
O A:HOH901 4.9 32.5 1.0
CG A:MET439 4.9 43.9 1.0
CB A:LEU485 4.9 29.2 1.0
C A:7DJ807 5.0 48.2 1.0
O A:HOH977 5.0 38.4 1.0

Fluorine binding site 5 out of 16 in 5tkb

Go back to Fluorine Binding Sites List in 5tkb
Fluorine binding site 5 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F707

b:69.4
occ:1.00
 F3 B:7DJ707 0.0 69.4 1.0
C13 B:7DJ707 1.3 70.4 1.0
C14 B:7DJ707 2.3 72.2 1.0
C12 B:7DJ707 2.4 69.4 1.0
F2 B:7DJ707 2.7 72.5 1.0
N5 B:7DJ707 2.8 63.2 1.0
N B:7DJ707 3.1 57.3 1.0
C1 B:7DJ707 3.1 58.9 1.0
CD1 B:ILE502 3.3 39.7 1.0
C17 B:7DJ707 3.6 73.4 1.0
C15 B:7DJ707 3.6 72.7 1.0
CG1 B:ILE502 3.7 37.4 1.0
CZ B:PHE506 3.7 38.7 1.0
CE1 B:HIS326 3.8 29.8 1.0
CE1 B:PHE506 4.0 39.4 1.0
N1 B:7DJ707 4.1 55.6 1.0
C16 B:7DJ707 4.1 73.2 1.0
NE2 B:HIS326 4.1 30.3 1.0
C B:7DJ707 4.2 56.5 1.0
N4 B:7DJ707 4.3 62.5 1.0
O2 B:7DJ707 4.5 73.3 1.0
F B:7DJ707 4.7 75.1 1.0
C6 B:7DJ707 4.8 54.4 1.0
CE2 B:PHE506 4.8 41.0 1.0
C2 B:7DJ707 4.9 54.6 1.0
CE1 B:TYR325 4.9 34.0 1.0
O B:HOH806 4.9 34.3 1.0
ND1 B:HIS326 4.9 29.9 1.0
O B:HOH854 5.0 31.4 1.0
C3 B:7DJ707 5.0 55.1 1.0

Fluorine binding site 6 out of 16 in 5tkb

Go back to Fluorine Binding Sites List in 5tkb
Fluorine binding site 6 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F707

b:72.5
occ:1.00
 F2 B:7DJ707 0.0 72.5 1.0
C14 B:7DJ707 1.4 72.2 1.0
C13 B:7DJ707 2.4 70.4 1.0
C15 B:7DJ707 2.4 72.7 1.0
F3 B:7DJ707 2.7 69.4 1.0
O B:HOH850 3.2 32.3 1.0
O2 B:7DJ707 3.5 73.3 1.0
C16 B:7DJ707 3.6 73.2 1.0
C12 B:7DJ707 3.6 69.4 1.0
CE1 B:HIS326 3.9 29.8 1.0
C17 B:7DJ707 4.1 73.4 1.0
O B:HOH856 4.1 34.1 1.0
NE2 B:HIS326 4.2 30.3 1.0
O B:HOH825 4.6 42.4 1.0
O B:HOH865 4.6 45.9 1.0
CE1 B:PHE506 4.6 39.4 1.0
F1 B:7DJ707 4.7 72.4 1.0
CZ B:PHE506 4.8 38.7 1.0
N5 B:7DJ707 4.8 63.2 1.0
C9 B:7DJ707 4.9 70.9 1.0

Fluorine binding site 7 out of 16 in 5tkb

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Fluorine binding site 7 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F707

b:72.4
occ:1.00
 F1 B:7DJ707 0.0 72.4 1.0
C16 B:7DJ707 1.4 73.2 1.0
C17 B:7DJ707 2.3 73.4 1.0
C15 B:7DJ707 2.4 72.7 1.0
F B:7DJ707 2.7 75.1 1.0
O B:HOH840 3.3 38.0 1.0
O B:THR437 3.5 42.8 1.0
CG B:MET439 3.5 47.8 1.0
C14 B:7DJ707 3.6 72.2 1.0
OD2 B:ASP484 3.6 45.0 1.0
O B:HOH826 3.6 33.0 1.0
C12 B:7DJ707 3.6 69.4 1.0
O B:HOH812 3.7 38.0 1.0
O B:HOH854 3.8 31.4 1.0
O B:HOH865 3.8 45.9 1.0
O B:HOH856 3.9 34.1 1.0
C13 B:7DJ707 4.1 70.4 1.0
SD B:MET439 4.1 51.5 1.0
CG B:ASP484 4.5 41.7 1.0
MG B:MG702 4.5 27.4 1.0
F2 B:7DJ707 4.7 72.5 1.0
CB B:MET439 4.7 43.9 1.0
C B:THR437 4.7 41.1 1.0
N B:MET439 4.8 41.0 1.0
N5 B:7DJ707 4.8 63.2 1.0
O B:HOH806 4.9 34.3 1.0
CD2 B:LEU485 4.9 49.3 1.0
OD1 B:ASP484 4.9 39.2 1.0

Fluorine binding site 8 out of 16 in 5tkb

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Fluorine binding site 8 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


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 Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F707

b:75.1
occ:1.00
 F B:7DJ707 0.0 75.1 1.0
C17 B:7DJ707 1.3 73.4 1.0
C16 B:7DJ707 2.3 73.2 1.0
C12 B:7DJ707 2.4 69.4 1.0
F1 B:7DJ707 2.7 72.4 1.0
O B:HOH806 2.8 34.3 1.0
N5 B:7DJ707 2.8 63.2 1.0
CD2 B:LEU485 3.1 49.3 1.0
O B:HOH854 3.5 31.4 1.0
C13 B:7DJ707 3.6 70.4 1.0
C15 B:7DJ707 3.6 72.7 1.0
O B:ASP484 3.9 36.0 1.0
OD2 B:ASP484 3.9 45.0 1.0
C1 B:7DJ707 4.0 58.9 1.0
CG B:ASP484 4.0 41.7 1.0
C14 B:7DJ707 4.1 72.2 1.0
CG B:LEU485 4.1 42.4 1.0
OD1 B:ASP484 4.2 39.2 1.0
C B:ASP484 4.3 39.0 1.0
O B:HOH840 4.4 38.0 1.0
N B:7DJ707 4.5 57.3 1.0
CB B:ASP484 4.7 35.8 1.0
F3 B:7DJ707 4.7 69.4 1.0
O B:HOH812 4.7 38.0 1.0
N B:LEU485 4.8 36.5 1.0
CA B:LEU485 4.8 36.2 1.0
SD B:MET439 4.9 51.5 1.0
C B:7DJ707 5.0 56.5 1.0
CZ B:PHE538 5.0 43.4 1.0

Fluorine binding site 9 out of 16 in 5tkb

Go back to Fluorine Binding Sites List in 5tkb
Fluorine binding site 9 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F705

b:68.9
occ:1.00
 F3 C:7DJ705 0.0 68.9 1.0
C13 C:7DJ705 1.3 68.7 1.0
C14 C:7DJ705 2.3 69.7 1.0
C12 C:7DJ705 2.4 66.6 1.0
F2 C:7DJ705 2.7 69.9 1.0
N5 C:7DJ705 2.8 60.6 1.0
N C:7DJ705 3.0 53.0 1.0
C1 C:7DJ705 3.1 55.6 1.0
CD1 C:ILE502 3.2 32.6 1.0
CG1 C:ILE502 3.6 33.6 1.0
C17 C:7DJ705 3.6 69.8 1.0
C15 C:7DJ705 3.6 70.8 1.0
CZ C:PHE506 3.7 36.3 1.0
CE1 C:HIS326 3.8 26.7 1.0
CE1 C:PHE506 3.9 37.2 1.0
N1 C:7DJ705 4.0 52.9 1.0
C16 C:7DJ705 4.1 70.7 1.0
O2 C:7DJ705 4.1 63.6 1.0
C C:7DJ705 4.2 52.4 1.0
NE2 C:HIS326 4.2 27.3 1.0
N4 C:7DJ705 4.4 58.1 1.0
F C:7DJ705 4.7 70.7 1.0
C6 C:7DJ705 4.8 52.8 1.0
CE2 C:PHE506 4.8 38.1 1.0
C2 C:7DJ705 4.9 53.0 1.0
CE1 C:TYR325 4.9 27.3 1.0
C3 C:7DJ705 5.0 52.7 1.0
CB C:ILE502 5.0 32.8 1.0
O C:HOH868 5.0 35.9 1.0
ND1 C:HIS326 5.0 28.0 1.0

Fluorine binding site 10 out of 16 in 5tkb

Go back to Fluorine Binding Sites List in 5tkb
Fluorine binding site 10 out of 16 in the Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Phosphodiesterase 4D in Complex with A Tetrafluoranline Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F705

b:69.9
occ:1.00
 F2 C:7DJ705 0.0 69.9 1.0
C14 C:7DJ705 1.4 69.7 1.0
C13 C:7DJ705 2.3 68.7 1.0
C15 C:7DJ705 2.4 70.8 1.0
F3 C:7DJ705 2.7 68.9 1.0
O2 C:7DJ705 3.1 63.6 1.0
O C:HOH867 3.4 30.4 1.0
C16 C:7DJ705 3.6 70.7 1.0
C12 C:7DJ705 3.6 66.6 1.0
CE1 C:HIS326 3.9 26.7 1.0
C17 C:7DJ705 4.1 69.8 1.0
NE2 C:HIS326 4.2 27.3 1.0
O C:HOH871 4.2 26.3 1.0
O C:HOH854 4.5 31.6 1.0
C9 C:7DJ705 4.5 63.5 1.0
CE1 C:PHE506 4.6 37.2 1.0
O C:HOH858 4.7 38.8 1.0
F1 C:7DJ705 4.7 69.4 1.0
CZ C:PHE506 4.7 36.3 1.0
N5 C:7DJ705 4.8 60.6 1.0

Reference:

R.Moslin, D.Gardner, J.Santella, Y.Zhang, J.V.Duncia, C.Liu, J.Lin, J.S.Tokarski, J.Strnad, D.Pedicord, J.Chen, Y.Blat, A.Zupa-Fernandez, L.Cheng, H.Sun, C.Chaudhry, C.Huang, C.D'arienzo, J.S.Sack, J.K.Muckelbauer, C.Chang, J.Tredup, D.Xie, N.Aranibar, J.R.Burke, P.H.Carter, D.S.Weinstein. Identification of Imidazo[1,2-B]Pyridazine TYK2 Pseudokinase Ligands As Potent and Selective Allosteric Inhibitors of TYK2 Signalling. Medchemcomm V. 8 700 2017.
ISSN: ISSN 2040-2503
PubMed: 30108788
DOI: 10.1039/C6MD00560H
Page generated: Thu Aug 1 15:13:31 2024

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