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Fluorine in PDB 5sfe: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe was solved by C.Joseph, L.Gobbi, 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) 43.75 / 1.86
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.85, 135.85, 235.666, 90, 90, 120
R / Rfree (%) 17.9 / 22.1

Other elements in 5sfe:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide (pdb code 5sfe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 5sfe

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Fluorine binding site 1 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:48.0
occ:0.50
 F16 A:WP3803 0.0 48.0 0.5
C13 A:WP3803 0.6 37.6 0.5
C14 A:WP3803 1.4 41.1 0.5
C12 A:WP3803 1.8 39.4 0.5
C15 A:WP3803 1.8 35.2 0.5
C11 A:WP3803 2.4 37.5 0.5
C12 A:WP3803 2.4 43.0 0.5
O A:HOH933 2.9 34.3 1.0
C14 A:WP3803 3.0 36.4 0.5
C10 A:WP3803 3.0 31.4 0.5
O A:LYS718 3.0 46.1 1.0
N A:VAL722 3.4 39.4 1.0
C11 A:WP3803 3.4 33.3 0.5
CG2 A:VAL722 3.4 39.0 1.0
CA A:VAL722 3.6 34.8 1.0
C A:GLU721 3.6 41.7 1.0
C10 A:WP3803 3.6 36.7 0.5
C13 A:WP3803 3.7 39.6 0.5
O A:GLU721 3.8 40.1 1.0
C A:LYS718 3.9 40.5 1.0
CB A:GLU721 4.1 51.1 1.0
O A:PRO712 4.1 33.1 1.0
F16 A:WP3803 4.1 37.7 0.5
CB A:VAL722 4.1 34.8 1.0
C15 A:WP3803 4.2 43.4 0.5
CA A:GLU721 4.2 42.8 1.0
C8 A:WP3803 4.2 31.2 0.5
N A:GLU721 4.3 42.5 1.0
O A:LYS719 4.5 42.2 1.0
CA A:LYS719 4.5 40.7 1.0
N A:LYS719 4.5 36.4 1.0
C A:LYS719 4.6 41.9 1.0
N9 A:WP3803 4.6 29.4 0.5
CB A:LYS718 4.6 42.2 1.0
CA A:MET713 4.7 36.9 1.0
C A:PRO712 4.7 34.1 1.0
CE1 A:TYR693 4.8 32.3 1.0
C8 A:WP3803 4.8 34.1 0.5
C A:VAL722 4.8 32.4 1.0
CA A:LYS718 4.9 40.5 1.0

Fluorine binding site 2 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 2 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:37.7
occ:0.50
 F16 A:WP3803 0.0 37.7 0.5
C14 A:WP3803 1.4 36.4 0.5
C13 A:WP3803 1.5 39.6 0.5
C12 A:WP3803 1.8 43.0 0.5
C11 A:WP3803 2.4 33.3 0.5
C12 A:WP3803 2.4 39.4 0.5
C15 A:WP3803 2.9 43.4 0.5
C14 A:WP3803 3.2 41.1 0.5
O A:HOH980 3.4 44.8 1.0
CB A:PRO712 3.4 45.5 1.0
CB A:GLU721 3.5 51.1 1.0
C13 A:WP3803 3.7 37.6 0.5
C10 A:WP3803 3.7 31.4 0.5
C10 A:WP3803 3.9 36.7 0.5
C11 A:WP3803 4.1 37.5 0.5
CG A:GLU721 4.1 58.7 1.0
F16 A:WP3803 4.1 48.0 0.5
C15 A:WP3803 4.2 35.2 0.5
CG A:PRO712 4.5 46.1 1.0
O A:GLU721 4.5 40.1 1.0
O A:HOH1078 4.6 50.6 1.0
CA A:PRO712 4.6 39.6 1.0
CA A:GLU721 4.8 42.8 1.0
C A:PRO712 4.8 34.1 1.0
CB A:LYS718 4.8 42.2 1.0
O A:LYS718 4.9 46.1 1.0
C8 A:WP3803 4.9 31.2 0.5
C A:GLU721 4.9 41.7 1.0
O A:PRO712 5.0 33.1 1.0

Fluorine binding site 3 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 3 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:43.2
occ:1.00
 F16 B:WP3803 0.0 43.2 1.0
C14 B:WP3803 1.3 38.9 1.0
C12 B:WP3803 2.4 36.4 1.0
C11 B:WP3803 2.4 37.2 1.0
CB B:PRO712 3.2 40.7 1.0
O B:HOH1101 3.4 57.3 1.0
C13 B:WP3803 3.6 35.3 1.0
C10 B:WP3803 3.6 33.4 1.0
OE2 B:GLU721 3.8 63.9 1.0
CB B:GLU721 3.9 46.9 1.0
CD B:GLU721 4.0 64.5 1.0
C15 B:WP3803 4.1 32.0 1.0
CG B:PRO712 4.1 38.6 1.0
OE1 B:GLU721 4.3 68.1 1.0
O B:HOH1099 4.4 48.0 1.0
CG B:GLU721 4.5 59.8 1.0
CA B:PRO712 4.5 34.0 1.0
C B:PRO712 4.6 30.9 1.0
O B:GLU721 4.7 32.1 1.0
C8 B:WP3803 4.8 31.2 1.0
CB B:LYS718 4.9 38.8 1.0
O B:PRO712 4.9 32.4 1.0
O B:LYS718 5.0 40.9 1.0

Fluorine binding site 4 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 4 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:53.4
occ:0.50
 F16 C:WP3803 0.0 53.4 0.5
C13 C:WP3803 1.0 35.0 0.5
C14 C:WP3803 1.4 50.5 0.5
C15 C:WP3803 2.0 36.6 0.5
C12 C:WP3803 2.1 35.1 0.5
C11 C:WP3803 2.3 49.5 0.5
C12 C:WP3803 2.4 50.1 0.5
N C:VAL722 2.9 42.0 1.0
CG2 C:VAL722 3.0 32.8 1.0
CA C:VAL722 3.1 41.8 1.0
O C:LYS718 3.1 41.8 1.0
C10 C:WP3803 3.2 34.0 0.5
C C:GLU721 3.2 45.4 1.0
O C:HOH946 3.3 39.0 1.0
C14 C:WP3803 3.3 36.5 0.5
O C:GLU721 3.5 41.3 1.0
C10 C:WP3803 3.6 47.4 0.5
CB C:VAL722 3.7 36.5 1.0
C13 C:WP3803 3.7 49.9 0.5
C11 C:WP3803 3.7 34.4 0.5
C C:LYS718 4.0 41.8 1.0
O C:LYS719 4.0 42.8 1.0
CA C:LYS719 4.1 36.9 1.0
CA C:GLU721 4.1 48.0 1.0
C C:LYS719 4.1 41.8 1.0
C15 C:WP3803 4.1 48.4 0.5
N C:GLU721 4.2 45.4 1.0
CB C:GLU721 4.2 51.9 1.0
C8 C:WP3803 4.4 34.2 0.5
C C:VAL722 4.4 38.9 1.0
N C:LYS719 4.4 37.1 1.0
F16 C:WP3803 4.5 37.1 0.5
O C:PRO712 4.5 38.6 1.0
C8 C:WP3803 4.8 44.4 0.5
N9 C:WP3803 4.8 30.0 0.5
CE1 C:TYR693 4.8 32.2 1.0
O C:VAL722 4.8 35.9 1.0
CG1 C:VAL722 4.9 38.3 1.0
OH C:TYR693 4.9 29.3 1.0
N9 C:WP3803 5.0 38.5 0.5

Fluorine binding site 5 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 5 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:37.1
occ:0.50
 F16 C:WP3803 0.0 37.1 0.5
C13 C:WP3803 1.4 49.9 0.5
C14 C:WP3803 1.4 36.5 0.5
C12 C:WP3803 2.1 50.1 0.5
C12 C:WP3803 2.4 35.1 0.5
C11 C:WP3803 2.4 34.4 0.5
C15 C:WP3803 2.5 48.4 0.5
CB C:PRO712 3.3 51.7 1.0
C14 C:WP3803 3.4 50.5 0.5
C13 C:WP3803 3.6 35.0 0.5
C10 C:WP3803 3.7 34.0 0.5
C10 C:WP3803 3.7 47.4 0.5
OE1 C:GLU721 3.8 79.3 1.0
CD C:GLU721 3.9 71.4 1.0
CB C:GLU721 3.9 51.9 1.0
OE2 C:GLU721 4.0 77.1 1.0
C11 C:WP3803 4.0 49.5 0.5
C15 C:WP3803 4.2 36.6 0.5
CG C:PRO712 4.3 45.5 1.0
F16 C:WP3803 4.5 53.4 0.5
CA C:PRO712 4.5 45.9 1.0
CG C:GLU721 4.5 63.1 1.0
O C:GLU721 4.6 41.3 1.0
C C:PRO712 4.6 40.8 1.0
O C:PRO712 4.8 38.6 1.0
O C:LYS718 4.9 41.8 1.0
C8 C:WP3803 4.9 34.2 0.5
CB C:LYS718 5.0 46.5 1.0

Fluorine binding site 6 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 6 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:67.8
occ:0.50
 F16 D:WP3803 0.0 67.8 0.5
C13 D:WP3803 1.0 46.5 0.5
C14 D:WP3803 1.4 60.4 0.5
C12 D:WP3803 2.0 46.3 0.5
C15 D:WP3803 2.2 44.8 0.5
C11 D:WP3803 2.4 55.9 0.5
C12 D:WP3803 2.4 59.3 0.5
O D:HOH930 2.7 41.1 1.0
O D:LYS718 2.9 53.4 1.0
C14 D:WP3803 3.3 42.0 0.5
C10 D:WP3803 3.4 43.4 0.5
N D:VAL722 3.5 46.6 1.0
C D:GLU721 3.6 55.5 1.0
C D:LYS718 3.6 43.3 1.0
C10 D:WP3803 3.6 52.4 0.5
C13 D:WP3803 3.6 54.2 0.5
CG2 D:VAL722 3.7 49.0 1.0
C11 D:WP3803 3.8 41.9 0.5
CA D:VAL722 3.8 51.5 1.0
O D:GLU721 3.9 54.8 1.0
O D:PRO712 4.0 41.1 1.0
C15 D:WP3803 4.1 53.3 0.5
O D:LYS719 4.2 52.2 1.0
N D:LYS719 4.2 52.6 1.0
N D:GLU721 4.2 52.1 1.0
CB D:LYS718 4.3 50.1 1.0
CA D:GLU721 4.3 51.2 1.0
C D:LYS719 4.3 58.8 1.0
CB D:VAL722 4.4 46.1 1.0
CA D:LYS719 4.4 54.4 1.0
CB D:GLU721 4.4 60.6 1.0
F16 D:WP3803 4.4 41.5 0.5
CA D:LYS718 4.5 48.4 1.0
C8 D:WP3803 4.6 40.8 0.5
C D:PRO712 4.7 41.6 1.0
CA D:MET713 4.8 46.6 1.0
O D:ASP715 4.8 42.5 1.0
C8 D:WP3803 4.8 47.5 0.5
CE1 D:TYR693 4.9 42.0 1.0
O D:MET713 5.0 48.3 1.0
N9 D:WP3803 5.0 42.3 0.5

Fluorine binding site 7 out of 7 in 5sfe

Go back to Fluorine Binding Sites List in 5sfe
Fluorine binding site 7 out of 7 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:41.5
occ:0.50
 F16 D:WP3803 0.0 41.5 0.5
C13 D:WP3803 1.3 54.2 0.5
C14 D:WP3803 1.4 42.0 0.5
C12 D:WP3803 2.1 59.3 0.5
C11 D:WP3803 2.4 41.9 0.5
C12 D:WP3803 2.4 46.3 0.5
C15 D:WP3803 2.5 53.3 0.5
CB D:PRO712 3.2 50.4 1.0
C14 D:WP3803 3.4 60.4 0.5
C10 D:WP3803 3.7 52.4 0.5
C13 D:WP3803 3.7 46.5 0.5
C10 D:WP3803 3.7 43.4 0.5
OE1 D:GLU721 3.9 76.3 1.0
C11 D:WP3803 4.0 55.9 0.5
CB D:GLU721 4.1 60.6 1.0
CG D:PRO712 4.2 50.8 1.0
C15 D:WP3803 4.2 44.8 0.5
O D:HOH1025 4.3 54.1 1.0
CD D:GLU721 4.4 71.5 1.0
F16 D:WP3803 4.4 67.8 0.5
CA D:PRO712 4.5 50.0 1.0
O D:GLU721 4.6 54.8 1.0
C D:PRO712 4.6 41.6 1.0
O D:PRO712 4.8 41.1 1.0
C8 D:WP3803 4.9 40.8 0.5
OE2 D:GLU721 4.9 85.3 1.0
C8 D:WP3803 4.9 47.5 0.5
CG D:GLU721 4.9 61.5 1.0
N D:MET713 5.0 41.6 1.0
CB D:LYS718 5.0 50.1 1.0

Reference:

L.Gobbi, J.Benz, D.Schlatter, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Tue Jul 15 07:10:30 2025

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