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Fluorine in PDB 5skf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile, PDB code: 5skf was solved by C.Joseph, J.Benz, A.Flohr, R.M.Rodriguez-Sarmiento, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.07 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.05, 135.05, 234.4, 90, 90, 120
R / Rfree (%) 17.1 / 18.7

Other elements in 5skf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 4 atoms
Praseodymium (Pr) 8 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile (pdb code 5skf). 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 Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile, PDB code: 5skf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F805

b:39.6
occ:1.00
 F23 A:KF9805 0.0 39.6 1.0
C7 A:KF9805 1.4 37.5 1.0
F24 A:KF9805 2.3 39.1 1.0
O10 A:KF9805 2.3 39.8 1.0
O9 A:KF9805 2.4 40.6 1.0
C6 A:KF9805 3.2 38.8 1.0
C13 A:KF9805 3.2 39.5 1.0
CG2 A:VAL733 3.6 32.9 1.0
CD1 A:PHE729 3.9 34.7 1.0
CE1 A:PHE729 4.3 34.9 1.0
C8 A:KF9805 4.5 36.7 1.0
C27 A:KF9805 4.5 38.4 1.0
CZ A:PHE639 4.7 30.3 1.0
CG A:PHE729 5.0 34.3 1.0

Fluorine binding site 2 out of 8 in 5skf

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F805

b:39.1
occ:1.00
 F24 A:KF9805 0.0 39.1 1.0
C7 A:KF9805 1.4 37.5 1.0
F23 A:KF9805 2.3 39.6 1.0
O9 A:KF9805 2.3 40.6 1.0
O10 A:KF9805 2.3 39.8 1.0
C6 A:KF9805 3.3 38.8 1.0
C13 A:KF9805 3.3 39.5 1.0
SD A:MET713 3.9 52.8 1.0
CE A:MET713 4.6 51.2 1.0
C8 A:KF9805 4.6 36.7 1.0
C27 A:KF9805 4.6 38.4 1.0
C14 A:KF9805 4.9 35.5 1.0

Fluorine binding site 3 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F808

b:43.2
occ:1.00
 F23 B:KF9808 0.0 43.2 1.0
C7 B:KF9808 1.4 41.5 1.0
O10 B:KF9808 2.3 44.2 1.0
F24 B:KF9808 2.3 43.9 1.0
O9 B:KF9808 2.4 43.4 1.0
C13 B:KF9808 3.1 41.4 1.0
C6 B:KF9808 3.1 40.8 1.0
CG2 B:VAL733 3.8 31.4 1.0
CD1 B:PHE729 3.9 29.7 1.0
CE1 B:PHE729 4.3 29.7 1.0
C27 B:KF9808 4.3 42.0 1.0
C8 B:KF9808 4.4 37.2 1.0
CZ B:PHE639 4.4 32.7 1.0
CD2 B:LEU635 4.5 30.6 1.0

Fluorine binding site 4 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F808

b:43.9
occ:1.00
 F24 B:KF9808 0.0 43.9 1.0
C7 B:KF9808 1.4 41.5 1.0
F23 B:KF9808 2.3 43.2 1.0
O9 B:KF9808 2.3 43.4 1.0
O10 B:KF9808 2.3 44.2 1.0
C6 B:KF9808 3.3 40.8 1.0
C13 B:KF9808 3.3 41.4 1.0
SD B:MET713 4.1 45.2 1.0
CE B:MET713 4.4 44.6 1.0
C8 B:KF9808 4.6 37.2 1.0
C27 B:KF9808 4.6 42.0 1.0
C14 B:KF9808 5.0 32.4 1.0

Fluorine binding site 5 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F806

b:45.1
occ:1.00
 F23 C:KF9806 0.0 45.1 1.0
C7 C:KF9806 1.4 42.2 1.0
F24 C:KF9806 2.3 44.5 1.0
O10 C:KF9806 2.3 42.8 1.0
O9 C:KF9806 2.3 42.5 1.0
C6 C:KF9806 3.1 40.5 1.0
C13 C:KF9806 3.1 40.0 1.0
CG2 C:VAL733 3.6 37.8 1.0
CD1 C:PHE729 3.8 37.0 1.0
CE1 C:PHE729 4.2 36.8 1.0
C8 C:KF9806 4.4 37.4 1.0
C27 C:KF9806 4.4 39.7 1.0
CZ C:PHE639 4.6 39.8 1.0
CB C:VAL733 4.8 36.8 1.0
CD1 C:LEU635 4.9 40.1 1.0
CG C:PHE729 5.0 38.3 1.0

Fluorine binding site 6 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F806

b:44.5
occ:1.00
 F24 C:KF9806 0.0 44.5 1.0
C7 C:KF9806 1.4 42.2 1.0
O9 C:KF9806 2.3 42.5 1.0
F23 C:KF9806 2.3 45.1 1.0
O10 C:KF9806 2.3 42.8 1.0
C6 C:KF9806 3.3 40.5 1.0
C13 C:KF9806 3.3 40.0 1.0
SD C:MET713 4.0 48.4 1.0
CE C:MET713 4.6 48.9 1.0
C8 C:KF9806 4.6 37.4 1.0
C27 C:KF9806 4.6 39.7 1.0
C14 C:KF9806 4.9 32.4 1.0

Fluorine binding site 7 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:47.5
occ:1.00
 F23 D:KF9803 0.0 47.5 1.0
C7 D:KF9803 1.4 44.9 1.0
F24 D:KF9803 2.3 49.6 1.0
O10 D:KF9803 2.3 40.6 1.0
O9 D:KF9803 2.3 42.6 1.0
C13 D:KF9803 3.2 40.8 1.0
C6 D:KF9803 3.2 38.0 1.0
CG2 D:VAL733 3.6 36.8 1.0
CD1 D:PHE729 3.9 40.7 1.0
CE1 D:PHE729 4.4 39.2 1.0
C8 D:KF9803 4.5 37.8 1.0
C27 D:KF9803 4.5 38.6 1.0
CZ D:PHE639 4.8 43.7 1.0
CB D:VAL733 4.9 38.1 1.0

Fluorine binding site 8 out of 8 in 5skf

Go back to Fluorine Binding Sites List in 5skf
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile


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 10 in Complex with 3-[5- [1-(2,2-Difluoro-1,3-Benzodioxol-4-Yl)-4-Oxopyridazin-3-Yl]Pyrazol-1- Yl]Benzonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:49.6
occ:1.00
 F24 D:KF9803 0.0 49.6 1.0
C7 D:KF9803 1.4 44.9 1.0
F23 D:KF9803 2.3 47.5 1.0
O9 D:KF9803 2.3 42.6 1.0
O10 D:KF9803 2.4 40.6 1.0
C6 D:KF9803 3.3 38.0 1.0
C13 D:KF9803 3.3 40.8 1.0
SD D:MET713 3.7 53.0 1.0
CE D:MET713 4.3 52.7 1.0
C8 D:KF9803 4.5 37.8 1.0
C27 D:KF9803 4.6 38.6 1.0
C14 D:KF9803 4.7 35.5 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Tue Jul 15 07:25:41 2025

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