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Fluorine in PDB 5skd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skd was solved by C.Joseph, J.Benz, A.Flohr, M.Rogers-Evans, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.61 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.64, 135.64, 234.83, 90, 90, 120
R / Rfree (%) 16.3 / 17.8

Other elements in 5skd:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One also contains other interesting chemical elements:

Praseodymium (Pr) 8 atoms
Zinc (Zn) 4 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One (pdb code 5skd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 25 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 25 in 5skd

Go back to Fluorine Binding Sites List in 5skd
Fluorine binding site 1 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:51.2
occ:1.00
 F19 A:KER803 0.0 51.2 1.0
C14 A:KER803 1.4 49.5 1.0
O17 A:KER803 2.2 47.6 1.0
F21 A:KER803 2.3 49.7 1.0
C18 A:KER803 2.5 45.0 1.0
F20 A:KER803 2.5 51.4 1.0
C24 A:KER803 2.7 42.7 1.0
C16 A:KER803 3.4 39.4 1.0
CD2 A:LEU635 3.6 35.2 1.0
C23 A:KER803 3.8 42.2 1.0
CZ A:PHE639 3.8 33.6 1.0
CG A:LEU635 4.2 34.1 1.0
CE2 A:PHE639 4.2 37.0 1.0
C15 A:KER803 4.4 40.0 1.0
C22 A:KER803 4.5 45.0 1.0
CG2 A:VAL733 4.5 30.8 1.0
CB A:LEU635 4.9 35.0 1.0

Fluorine binding site 2 out of 25 in 5skd

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Fluorine binding site 2 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:51.4
occ:1.00
 F20 A:KER803 0.0 51.4 1.0
C14 A:KER803 1.4 49.5 1.0
F21 A:KER803 2.2 49.7 1.0
O17 A:KER803 2.2 47.6 1.0
F19 A:KER803 2.5 51.2 1.0
C18 A:KER803 3.0 45.0 1.0
C16 A:KER803 3.3 39.4 1.0
CG2 A:VAL733 3.7 30.8 1.0
C24 A:KER803 4.1 42.7 1.0
CD1 A:PHE729 4.3 39.1 1.0
C15 A:KER803 4.6 40.0 1.0
CZ A:PHE639 4.6 33.6 1.0
CE1 A:PHE729 4.9 37.2 1.0

Fluorine binding site 3 out of 25 in 5skd

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Fluorine binding site 3 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:49.7
occ:1.00
 F21 A:KER803 0.0 49.7 1.0
C14 A:KER803 1.4 49.5 1.0
F20 A:KER803 2.2 51.4 1.0
F19 A:KER803 2.3 51.2 1.0
O17 A:KER803 2.3 47.6 1.0
C18 A:KER803 3.5 45.0 1.0
CZ A:PHE639 4.1 33.6 1.0
C24 A:KER803 4.2 42.7 1.0
C16 A:KER803 4.5 39.4 1.0
CE2 A:PHE639 4.5 37.0 1.0

Fluorine binding site 4 out of 25 in 5skd

Go back to Fluorine Binding Sites List in 5skd
Fluorine binding site 4 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:45.7
occ:1.00
 F28 A:KER803 0.0 45.7 1.0
C25 A:KER803 1.4 40.9 1.0
C27 A:KER803 2.4 38.3 1.0
C13 A:KER803 2.4 41.2 1.0
CG2 A:ILE692 2.6 34.6 1.0
N9 A:KER803 2.8 46.0 1.0
C8 A:KER803 3.3 39.0 1.0
CG1 A:ILE692 3.4 36.4 1.0
CZ A:PHE696 3.4 33.3 1.0
CB A:ILE692 3.5 34.4 1.0
CD1 A:ILE692 3.6 33.4 1.0
C5 A:KER803 3.6 39.9 1.0
C30 A:KER803 3.6 40.7 1.0
C26 A:KER803 3.7 48.6 1.0
N10 A:KER803 3.7 42.8 1.0
N4 A:KER803 3.9 48.3 1.0
CE2 A:PHE696 4.1 34.5 1.0
CE1 A:PHE696 4.1 33.1 1.0
C29 A:KER803 4.1 48.0 1.0
CE2 A:TYR524 4.2 31.1 1.0
C12 A:KER803 4.3 37.6 1.0
C6 A:KER803 4.4 38.0 1.0
CA A:ILE692 4.4 34.1 1.0
C11 A:KER803 4.5 39.5 1.0
CD2 A:TYR524 4.5 31.2 1.0
N3 A:KER803 4.7 40.9 1.0
O7 A:KER803 4.8 34.5 1.0
CZ A:TYR524 4.8 33.5 1.0

Fluorine binding site 5 out of 25 in 5skd

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Fluorine binding site 5 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:59.2
occ:1.00
 F31 A:KER803 0.0 59.2 1.0
C29 A:KER803 1.4 48.0 1.0
C30 A:KER803 2.4 40.7 1.0
C26 A:KER803 2.4 48.6 1.0
O A:HOH944 3.4 30.7 1.0
C27 A:KER803 3.6 38.3 1.0
C13 A:KER803 3.6 41.2 1.0
O A:HOH978 4.0 35.4 1.0
C25 A:KER803 4.1 40.9 1.0
CD2 A:LEU635 4.2 35.2 1.0
O A:HOH995 4.3 22.2 1.0
CB A:LEU635 4.4 35.0 1.0
C22 A:KER803 4.4 45.0 1.0
C23 A:KER803 4.5 42.2 1.0
O A:HOH926 4.6 29.8 1.0
O A:HOH929 4.6 31.0 1.0
O A:HOH937 4.7 30.2 1.0
CG A:LEU635 4.8 34.1 1.0
O A:HOH981 4.8 49.7 1.0
O A:HOH950 4.8 27.9 1.0
N9 A:KER803 4.8 46.0 1.0
OD2 A:ASP674 4.8 28.6 1.0
CD2 A:LEU675 4.9 30.4 1.0
O A:THR633 5.0 32.0 1.0

Fluorine binding site 6 out of 25 in 5skd

Go back to Fluorine Binding Sites List in 5skd
Fluorine binding site 6 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:47.5
occ:0.50
 F19 B:KER809 0.0 47.5 0.5
F19 B:KER809 0.4 51.2 0.5
C14 B:KER809 1.2 51.5 0.5
C14 B:KER809 1.4 50.7 0.5
F20 B:KER809 2.0 50.0 0.5
F21 B:KER809 2.0 54.3 0.5
F21 B:KER809 2.3 52.1 0.5
F20 B:KER809 2.3 51.4 0.5
O17 B:KER809 2.3 49.4 0.5
O17 B:KER809 2.3 48.3 0.5
C18 B:KER809 2.7 47.5 0.5
C18 B:KER809 2.8 46.7 0.5
C24 B:KER809 3.0 43.1 0.5
C24 B:KER809 3.0 42.6 0.5
CD2 B:LEU635 3.6 35.6 1.0
CZ B:PHE639 3.7 31.4 1.0
C16 B:KER809 3.8 44.5 0.5
C16 B:KER809 3.8 42.8 0.5
CE2 B:PHE639 4.0 31.5 1.0
C23 B:KER809 4.2 44.0 0.5
C23 B:KER809 4.2 42.8 0.5
CG B:LEU635 4.5 32.1 1.0
CG2 B:VAL733 4.7 35.2 1.0
C15 B:KER809 4.7 42.8 0.5
C15 B:KER809 4.7 41.4 0.5
C22 B:KER809 4.9 41.9 0.5
C22 B:KER809 4.9 41.2 0.5
CE1 B:PHE639 4.9 38.2 1.0

Fluorine binding site 7 out of 25 in 5skd

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Fluorine binding site 7 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:51.2
occ:0.50
 F19 B:KER809 0.0 51.2 0.5
F19 B:KER809 0.4 47.5 0.5
C14 B:KER809 1.4 51.5 0.5
C14 B:KER809 1.6 50.7 0.5
F20 B:KER809 2.2 50.0 0.5
F21 B:KER809 2.2 54.3 0.5
O17 B:KER809 2.3 49.4 0.5
O17 B:KER809 2.3 48.3 0.5
F21 B:KER809 2.5 52.1 0.5
F20 B:KER809 2.5 51.4 0.5
C18 B:KER809 2.6 47.5 0.5
C18 B:KER809 2.7 46.7 0.5
C24 B:KER809 2.7 43.1 0.5
C24 B:KER809 2.8 42.6 0.5
CD2 B:LEU635 3.5 35.6 1.0
C16 B:KER809 3.7 44.5 0.5
C16 B:KER809 3.7 42.8 0.5
C23 B:KER809 3.9 44.0 0.5
C23 B:KER809 3.9 42.8 0.5
CZ B:PHE639 3.9 31.4 1.0
CE2 B:PHE639 4.1 31.5 1.0
CG B:LEU635 4.3 32.1 1.0
C15 B:KER809 4.6 42.8 0.5
C15 B:KER809 4.6 41.4 0.5
C22 B:KER809 4.6 41.9 0.5
C22 B:KER809 4.6 41.2 0.5
CB B:LEU635 4.8 28.3 1.0
CG2 B:VAL733 4.9 35.2 1.0

Fluorine binding site 8 out of 25 in 5skd

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Fluorine binding site 8 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:51.4
occ:0.50
 F20 B:KER809 0.0 51.4 0.5
F20 B:KER809 0.4 50.0 0.5
C14 B:KER809 1.4 50.7 0.5
C14 B:KER809 1.5 51.5 0.5
F19 B:KER809 2.3 47.5 0.5
F21 B:KER809 2.3 54.3 0.5
O17 B:KER809 2.3 49.4 0.5
F21 B:KER809 2.3 52.1 0.5
O17 B:KER809 2.3 48.3 0.5
F19 B:KER809 2.5 51.2 0.5
C18 B:KER809 3.0 46.7 0.5
C18 B:KER809 3.0 47.5 0.5
C16 B:KER809 3.2 42.8 0.5
C16 B:KER809 3.3 44.5 0.5
CG2 B:VAL733 3.8 35.2 1.0
CD1 B:PHE729 4.0 33.2 1.0
C24 B:KER809 4.0 42.6 0.5
C24 B:KER809 4.1 43.1 0.5
CE1 B:PHE729 4.4 33.2 1.0
CZ B:PHE639 4.4 31.4 1.0
C15 B:KER809 4.4 41.4 0.5
C15 B:KER809 4.5 42.8 0.5
CD2 B:LEU635 4.8 35.6 1.0

Fluorine binding site 9 out of 25 in 5skd

Go back to Fluorine Binding Sites List in 5skd
Fluorine binding site 9 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:50.0
occ:0.50
 F20 B:KER809 0.0 50.0 0.5
F20 B:KER809 0.4 51.4 0.5
C14 B:KER809 1.4 50.7 0.5
C14 B:KER809 1.4 51.5 0.5
F19 B:KER809 2.0 47.5 0.5
F19 B:KER809 2.2 51.2 0.5
O17 B:KER809 2.3 49.4 0.5
O17 B:KER809 2.4 48.3 0.5
F21 B:KER809 2.4 54.3 0.5
F21 B:KER809 2.4 52.1 0.5
C18 B:KER809 2.8 46.7 0.5
C18 B:KER809 2.9 47.5 0.5
C16 B:KER809 3.2 42.8 0.5
C16 B:KER809 3.2 44.5 0.5
CG2 B:VAL733 3.6 35.2 1.0
C24 B:KER809 3.8 42.6 0.5
C24 B:KER809 3.9 43.1 0.5
CD1 B:PHE729 3.9 33.2 1.0
CZ B:PHE639 4.2 31.4 1.0
CE1 B:PHE729 4.2 33.2 1.0
C15 B:KER809 4.3 41.4 0.5
C15 B:KER809 4.4 42.8 0.5
CD2 B:LEU635 4.4 35.6 1.0
C23 B:KER809 4.8 42.8 0.5
CB B:VAL733 4.8 33.9 1.0
C23 B:KER809 4.9 44.0 0.5
CE2 B:PHE639 5.0 31.5 1.0
C22 B:KER809 5.0 41.2 0.5
CE1 B:PHE639 5.0 38.2 1.0

Fluorine binding site 10 out of 25 in 5skd

Go back to Fluorine Binding Sites List in 5skd
Fluorine binding site 10 out of 25 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One


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 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F809

b:52.1
occ:0.50
 F21 B:KER809 0.0 52.1 0.5
F21 B:KER809 0.3 54.3 0.5
C14 B:KER809 1.4 50.7 0.5
C14 B:KER809 1.5 51.5 0.5
F19 B:KER809 2.3 47.5 0.5
O17 B:KER809 2.3 48.3 0.5
O17 B:KER809 2.3 49.4 0.5
F20 B:KER809 2.3 51.4 0.5
F20 B:KER809 2.4 50.0 0.5
F19 B:KER809 2.5 51.2 0.5
C18 B:KER809 3.6 46.7 0.5
C18 B:KER809 3.6 47.5 0.5
C24 B:KER809 4.3 43.1 0.5
C24 B:KER809 4.3 42.6 0.5
C16 B:KER809 4.5 42.8 0.5
C16 B:KER809 4.5 44.5 0.5
CZ B:PHE639 4.6 31.4 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: Thu Aug 1 14:34:28 2024

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