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Fluorine in PDB 5sf1: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1 was solved by C.Joseph, K.Groebke-Zbinden, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.74 / 2.11
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.436, 135.436, 235.715, 90, 90, 120
R / Rfree (%) 18.4 / 23.1

Other elements in 5sf1:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine (pdb code 5sf1). 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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine, PDB code: 5sf1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:47.5
occ:1.00
 F12 A:IJ0801 0.0 47.5 1.0
C11 A:IJ0801 1.4 47.8 1.0
F13 A:IJ0801 2.2 46.1 1.0
C8 A:IJ0801 2.3 38.7 1.0
C7 A:IJ0801 2.9 40.6 1.0
C10 A:IJ0801 3.1 40.5 1.0
CD1 A:ILE692 3.1 44.8 1.0
CB A:SER677 3.2 39.6 1.0
O A:HOH951 3.6 34.4 1.0
N9 A:IJ0801 3.6 38.8 1.0
O A:HOH937 3.7 36.1 1.0
CG1 A:VAL678 3.8 38.3 1.0
N A:VAL678 3.9 38.1 1.0
CA A:SER677 4.0 37.7 1.0
C A:SER677 4.0 36.5 1.0
OH A:TYR524 4.1 38.0 1.0
N6 A:IJ0801 4.2 39.0 1.0
OG A:SER677 4.3 40.0 1.0
O A:LEU675 4.3 32.2 1.0
N A:SER677 4.3 30.4 1.0
C5 A:IJ0801 4.5 37.7 1.0
CG1 A:ILE692 4.5 39.8 1.0
CZ A:TYR524 4.8 36.5 1.0
O A:SER677 4.8 38.9 1.0
CA A:VAL678 4.8 32.4 1.0
CB A:VAL678 4.8 37.8 1.0
C A:LEU675 4.9 33.0 1.0

Fluorine binding site 2 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 2 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:46.1
occ:1.00
 F13 A:IJ0801 0.0 46.1 1.0
C11 A:IJ0801 1.3 47.8 1.0
C8 A:IJ0801 2.2 38.7 1.0
F12 A:IJ0801 2.2 47.5 1.0
N9 A:IJ0801 2.9 38.8 1.0
O A:LEU675 3.0 32.2 1.0
CA A:LEU675 3.2 34.0 1.0
C7 A:IJ0801 3.3 40.6 1.0
C A:LEU675 3.4 33.0 1.0
O A:HOH937 3.5 36.1 1.0
CG1 A:VAL678 3.6 38.3 1.0
CB A:LEU675 3.6 38.7 1.0
CD2 A:LEU675 3.6 41.9 1.0
C10 A:IJ0801 4.0 40.5 1.0
C5 A:IJ0801 4.0 37.7 1.0
N6 A:IJ0801 4.2 39.0 1.0
CG A:LEU675 4.2 38.4 1.0
N A:VAL678 4.2 38.1 1.0
O A:ASP674 4.3 33.8 1.0
CE2 A:PHE729 4.3 36.5 1.0
N A:SER677 4.4 30.4 1.0
O A:HOH945 4.5 37.3 1.0
O A:HOH912 4.5 35.8 1.0
CB A:SER677 4.5 39.6 1.0
N A:LEU675 4.5 35.4 1.0
CB A:VAL678 4.6 37.8 1.0
OH A:TYR524 4.6 38.0 1.0
CG2 A:VAL678 4.6 36.8 1.0
CZ A:PHE729 4.6 39.6 1.0
N A:CYS676 4.6 35.5 1.0
CA A:SER677 4.8 37.7 1.0
C A:SER677 4.8 36.5 1.0
CD1 A:ILE692 4.9 44.8 1.0
C A:ASP674 4.9 34.1 1.0

Fluorine binding site 3 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:45.7
occ:1.00
 F12 B:IJ0801 0.0 45.7 1.0
C11 B:IJ0801 1.3 43.2 1.0
F13 B:IJ0801 2.1 48.6 1.0
C8 B:IJ0801 2.4 41.0 1.0
C7 B:IJ0801 2.9 38.9 1.0
CD1 B:ILE692 3.0 39.8 1.0
C10 B:IJ0801 3.0 41.5 1.0
CB B:SER677 3.3 41.1 1.0
N9 B:IJ0801 3.6 36.4 1.0
O B:HOH911 3.8 37.3 1.0
CG1 B:VAL678 3.8 38.0 1.0
O B:HOH955 3.9 32.4 1.0
OH B:TYR524 4.0 35.4 1.0
CA B:SER677 4.1 40.1 1.0
C B:SER677 4.1 42.1 1.0
N B:VAL678 4.1 42.1 1.0
N6 B:IJ0801 4.2 39.8 1.0
O B:LEU675 4.3 32.6 1.0
OG B:SER677 4.3 45.2 1.0
CG1 B:ILE692 4.4 43.1 1.0
N B:SER677 4.4 34.3 1.0
C5 B:IJ0801 4.5 37.5 1.0
CZ B:TYR524 4.6 35.4 1.0
O B:SER677 4.7 50.4 1.0
CE1 B:TYR524 4.9 35.4 1.0
CG2 B:THR688 4.9 31.5 1.0
C B:LEU675 4.9 30.0 1.0
CB B:VAL678 5.0 38.9 1.0

Fluorine binding site 4 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:48.6
occ:1.00
 F13 B:IJ0801 0.0 48.6 1.0
C11 B:IJ0801 1.2 43.2 1.0
F12 B:IJ0801 2.1 45.7 1.0
C8 B:IJ0801 2.2 41.0 1.0
N9 B:IJ0801 3.0 36.4 1.0
O B:LEU675 3.1 32.6 1.0
C7 B:IJ0801 3.3 38.9 1.0
CA B:LEU675 3.3 28.9 1.0
O B:HOH911 3.4 37.3 1.0
CD2 B:LEU675 3.5 33.1 1.0
C B:LEU675 3.5 30.0 1.0
CG1 B:VAL678 3.7 38.0 1.0
CB B:LEU675 3.7 30.8 1.0
C10 B:IJ0801 4.0 41.5 1.0
C5 B:IJ0801 4.0 37.5 1.0
N6 B:IJ0801 4.2 39.8 1.0
CG B:LEU675 4.2 33.5 1.0
N B:VAL678 4.3 42.1 1.0
O B:ASP674 4.3 28.4 1.0
OH B:TYR524 4.3 35.4 1.0
CB B:SER677 4.4 41.1 1.0
N B:SER677 4.4 34.3 1.0
CE2 B:PHE729 4.5 32.0 1.0
O B:HOH933 4.5 36.6 1.0
N B:LEU675 4.6 29.6 1.0
N B:CYS676 4.7 32.8 1.0
CA B:SER677 4.7 40.1 1.0
CB B:VAL678 4.7 38.9 1.0
CD1 B:ILE692 4.8 39.8 1.0
C B:SER677 4.8 42.1 1.0
CZ B:PHE729 4.8 32.5 1.0
CG2 B:VAL678 4.9 36.9 1.0
C B:ASP674 4.9 29.3 1.0

Fluorine binding site 5 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:39.9
occ:1.00
 F12 C:IJ0801 0.0 39.9 1.0
C11 C:IJ0801 1.3 35.6 1.0
F13 C:IJ0801 2.1 47.4 1.0
C8 C:IJ0801 2.3 31.2 1.0
C7 C:IJ0801 2.9 39.4 1.0
CB C:SER677 3.0 43.3 1.0
C10 C:IJ0801 3.0 40.6 1.0
CD1 C:ILE692 3.1 47.3 1.0
N9 C:IJ0801 3.6 36.7 1.0
CG1 C:VAL678 3.7 38.8 1.0
O C:HOH958 3.7 38.7 1.0
O C:HOH944 3.8 38.9 1.0
CA C:SER677 4.0 46.7 1.0
OH C:TYR524 4.1 35.8 1.0
C C:SER677 4.1 40.9 1.0
OG C:SER677 4.1 47.6 1.0
N C:VAL678 4.1 39.8 1.0
N6 C:IJ0801 4.1 40.0 1.0
O C:LEU675 4.3 30.2 1.0
N C:SER677 4.4 37.9 1.0
C5 C:IJ0801 4.5 35.2 1.0
CG1 C:ILE692 4.5 43.8 1.0
O C:SER677 4.7 47.6 1.0
CZ C:TYR524 4.8 36.2 1.0
C C:LEU675 4.8 29.8 1.0
CB C:VAL678 4.9 42.7 1.0
CA C:VAL678 4.9 39.6 1.0

Fluorine binding site 6 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F801

b:47.4
occ:1.00
 F13 C:IJ0801 0.0 47.4 1.0
C11 C:IJ0801 1.3 35.6 1.0
F12 C:IJ0801 2.1 39.9 1.0
C8 C:IJ0801 2.2 31.2 1.0
N9 C:IJ0801 3.0 36.7 1.0
O C:LEU675 3.2 30.2 1.0
CA C:LEU675 3.3 28.9 1.0
C7 C:IJ0801 3.3 39.4 1.0
C C:LEU675 3.5 29.8 1.0
O C:HOH944 3.5 38.9 1.0
CD2 C:LEU675 3.5 40.2 1.0
CB C:LEU675 3.7 35.6 1.0
CG1 C:VAL678 3.7 38.8 1.0
C5 C:IJ0801 4.1 35.2 1.0
C10 C:IJ0801 4.1 40.6 1.0
CB C:SER677 4.1 43.3 1.0
O C:ASP674 4.2 29.5 1.0
CG C:LEU675 4.2 36.3 1.0
N6 C:IJ0801 4.3 40.0 1.0
O C:HOH932 4.3 36.3 1.0
OH C:TYR524 4.3 35.8 1.0
N C:VAL678 4.4 39.8 1.0
CE2 C:PHE729 4.5 38.3 1.0
N C:SER677 4.5 37.9 1.0
N C:LEU675 4.5 32.6 1.0
N C:CYS676 4.6 33.5 1.0
CA C:SER677 4.7 46.7 1.0
CB C:VAL678 4.8 42.7 1.0
C C:ASP674 4.8 33.8 1.0
CZ C:PHE729 4.8 34.5 1.0
CD1 C:ILE692 4.8 47.3 1.0
C C:SER677 4.8 40.9 1.0
CG2 C:VAL678 4.9 42.0 1.0

Fluorine binding site 7 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F801

b:62.5
occ:1.00
 F12 D:IJ0801 0.0 62.5 1.0
C11 D:IJ0801 1.3 64.1 1.0
F13 D:IJ0801 2.1 73.5 1.0
C8 D:IJ0801 2.4 52.8 1.0
C7 D:IJ0801 3.0 57.9 1.0
CB D:SER677 3.0 59.7 1.0
C10 D:IJ0801 3.0 64.2 1.0
CD1 D:ILE692 3.1 55.9 1.0
O D:HOH905 3.7 46.5 1.0
N9 D:IJ0801 3.8 51.0 1.0
CA D:SER677 3.9 58.4 1.0
CG1 D:VAL678 3.9 60.1 1.0
N D:VAL678 4.0 53.3 1.0
C D:SER677 4.0 55.7 1.0
OG D:SER677 4.0 63.5 1.0
OH D:TYR524 4.1 54.9 1.0
O D:LEU675 4.1 44.9 1.0
N D:SER677 4.2 49.8 1.0
N6 D:IJ0801 4.3 58.0 1.0
CG1 D:ILE692 4.5 57.7 1.0
C5 D:IJ0801 4.6 50.5 1.0
CG2 D:THR688 4.7 49.0 1.0
O D:SER677 4.7 55.5 1.0
C D:LEU675 4.7 47.2 1.0
CZ D:TYR524 4.7 58.0 1.0
CA D:VAL678 4.9 53.7 1.0
CB D:VAL678 5.0 55.6 1.0
CE1 D:TYR524 5.0 54.2 1.0

Fluorine binding site 8 out of 8 in 5sf1

Go back to Fluorine Binding Sites List in 5sf1
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine


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 2- (Difluoromethyl)-3-Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl) Ethynyl]Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F801

b:73.5
occ:1.00
 F13 D:IJ0801 0.0 73.5 1.0
C11 D:IJ0801 1.2 64.1 1.0
F12 D:IJ0801 2.1 62.5 1.0
C8 D:IJ0801 2.2 52.8 1.0
O D:LEU675 2.9 44.9 1.0
N9 D:IJ0801 3.0 51.0 1.0
C7 D:IJ0801 3.2 57.9 1.0
CA D:LEU675 3.3 51.8 1.0
C D:LEU675 3.4 47.2 1.0
CD2 D:LEU675 3.7 58.7 1.0
CB D:LEU675 3.8 54.1 1.0
CG1 D:VAL678 3.9 60.1 1.0
C10 D:IJ0801 3.9 64.2 1.0
C5 D:IJ0801 4.1 50.5 1.0
N6 D:IJ0801 4.2 58.0 1.0
N D:VAL678 4.3 53.3 1.0
CB D:SER677 4.3 59.7 1.0
N D:SER677 4.3 49.8 1.0
CG D:LEU675 4.3 54.1 1.0
OH D:TYR524 4.4 54.9 1.0
O D:ASP674 4.4 46.3 1.0
N D:CYS676 4.4 44.0 1.0
O D:HOH904 4.5 45.5 1.0
N D:LEU675 4.6 54.0 1.0
CE2 D:PHE729 4.6 53.3 1.0
CG2 D:VAL678 4.7 52.2 1.0
CA D:SER677 4.7 58.4 1.0
CB D:VAL678 4.7 55.6 1.0
CZ D:PHE729 4.8 50.3 1.0
CD1 D:ILE692 4.8 55.9 1.0
C D:SER677 4.8 55.7 1.0
C D:ASP674 5.0 53.5 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Thu Aug 1 14:14:37 2024

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