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Fluorine in PDB 5sku: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid, PDB code: 5sku was solved by C.Joseph, J.Benz, A.Flohr, A.Binggeli, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.289, 135.289, 234.535, 90, 90, 120
R / Rfree (%) 18.1 / 22.5

Other elements in 5sku:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid 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-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid (pdb code 5sku). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid, PDB code: 5sku:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5sku

Go back to Fluorine Binding Sites List in 5sku
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:60.7
occ:1.00
 F7 A:KJ3803 0.0 60.7 1.0
C1 A:KJ3803 1.4 53.2 1.0
C6 A:KJ3803 2.4 50.7 1.0
C2 A:KJ3803 2.4 49.0 1.0
CB A:SER677 3.0 36.3 1.0
OG A:SER677 3.1 48.6 1.0
O A:HOH943 3.3 30.5 1.0
O A:LEU675 3.3 25.1 1.0
CG1 A:VAL678 3.6 31.3 1.0
C4 A:KJ3803 3.6 47.7 1.0
C5 A:KJ3803 3.7 51.3 1.0
N A:VAL678 3.7 29.6 1.0
CA A:SER677 3.8 32.5 1.0
C A:LEU675 3.9 28.4 1.0
N A:SER677 3.9 28.8 1.0
CD1 A:ILE692 4.0 37.8 1.0
C A:SER677 4.0 31.4 1.0
OH A:TYR524 4.1 34.9 1.0
CA A:LEU675 4.1 29.3 1.0
C3 A:KJ3803 4.1 47.4 1.0
O A:HOH925 4.3 24.9 1.0
CB A:VAL678 4.6 30.8 1.0
CA A:VAL678 4.6 29.9 1.0
CB A:LEU675 4.8 30.9 1.0
N A:CYS676 4.8 27.4 1.0
O8 A:KJ3803 4.9 55.3 1.0
O A:ASP674 4.9 27.8 1.0
CZ A:TYR524 5.0 31.2 1.0
O A:HOH1000 5.0 40.1 1.0
C A:CYS676 5.0 28.5 1.0

Fluorine binding site 2 out of 4 in 5sku

Go back to Fluorine Binding Sites List in 5sku
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:52.1
occ:1.00
 F7 B:KJ3803 0.0 52.1 1.0
C1 B:KJ3803 1.4 48.4 1.0
C6 B:KJ3803 2.4 47.8 1.0
C2 B:KJ3803 2.4 48.4 1.0
CB B:SER677 3.0 34.0 1.0
OG B:SER677 3.3 40.4 1.0
O B:HOH937 3.4 29.9 1.0
O B:LEU675 3.5 23.2 1.0
C4 B:KJ3803 3.6 46.4 1.0
CG1 B:VAL678 3.6 31.3 1.0
CD1 B:ILE692 3.6 35.9 1.0
C5 B:KJ3803 3.7 50.8 1.0
CA B:SER677 3.9 32.2 1.0
OH B:TYR524 3.9 31.2 1.0
N B:VAL678 3.9 30.9 1.0
N B:SER677 4.1 30.3 1.0
C3 B:KJ3803 4.1 45.7 1.0
C B:LEU675 4.2 24.2 1.0
C B:SER677 4.2 32.9 1.0
O B:HOH972 4.3 22.0 1.0
CA B:LEU675 4.4 24.8 1.0
CB B:VAL678 4.8 32.1 1.0
CZ B:TYR524 4.8 29.7 1.0
CA B:VAL678 4.8 32.7 1.0
O8 B:KJ3803 4.8 56.1 1.0
CD2 B:LEU675 4.9 30.3 1.0
O B:HOH1008 4.9 39.6 1.0
CG1 B:ILE692 4.9 34.9 1.0
CB B:LEU675 5.0 26.2 1.0

Fluorine binding site 3 out of 4 in 5sku

Go back to Fluorine Binding Sites List in 5sku
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:50.9
occ:1.00
 F7 C:KJ3803 0.0 50.9 1.0
C1 C:KJ3803 1.4 43.2 1.0
C2 C:KJ3803 2.3 42.6 1.0
C6 C:KJ3803 2.4 42.1 1.0
OG C:SER677 2.5 45.0 1.0
CB C:SER677 3.3 37.7 1.0
CG1 C:VAL678 3.6 30.5 1.0
C5 C:KJ3803 3.6 44.5 1.0
O C:LEU675 3.6 25.4 1.0
C4 C:KJ3803 3.7 39.8 1.0
CD1 C:ILE692 3.7 37.4 1.0
O C:HOH927 3.8 31.9 1.0
N C:VAL678 3.9 32.8 1.0
OH C:TYR524 4.0 35.6 1.0
CA C:SER677 4.0 34.5 1.0
O C:HOH971 4.1 27.3 1.0
C3 C:KJ3803 4.1 40.3 1.0
N C:SER677 4.1 31.4 1.0
C C:LEU675 4.2 25.9 1.0
C C:SER677 4.2 32.9 1.0
CA C:LEU675 4.4 27.8 1.0
CB C:VAL678 4.7 31.7 1.0
O8 C:KJ3803 4.7 51.0 1.0
CA C:VAL678 4.8 31.4 1.0
CZ C:TYR524 4.8 32.7 1.0
O C:HOH1009 4.9 38.1 1.0
CG1 C:ILE692 4.9 35.3 1.0
CB C:LEU675 5.0 29.9 1.0

Fluorine binding site 4 out of 4 in 5sku

Go back to Fluorine Binding Sites List in 5sku
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid


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-[4- [2-[2-(2-Ethoxy-4-Fluorophenyl)-5-Methyl-1,3-Oxazol-4- Yl]Ethoxy]Naphthalen-1-Yl]-2-Methoxypropanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:52.3
occ:1.00
 F7 D:KJ3803 0.0 52.3 1.0
C1 D:KJ3803 1.4 47.5 1.0
C2 D:KJ3803 2.4 47.1 1.0
OG D:SER677 2.4 49.0 1.0
C6 D:KJ3803 2.4 47.4 1.0
O D:HOH911 3.1 36.2 1.0
CB D:SER677 3.5 44.7 1.0
O D:LEU675 3.5 36.8 1.0
C5 D:KJ3803 3.6 49.8 1.0
CG1 D:VAL678 3.6 45.9 1.0
C4 D:KJ3803 3.6 46.1 1.0
OH D:TYR524 3.8 49.5 1.0
CD1 D:ILE692 3.8 42.4 1.0
C D:LEU675 3.9 38.1 1.0
N D:SER677 4.0 38.1 1.0
N D:VAL678 4.0 40.1 1.0
CA D:SER677 4.1 41.8 1.0
C3 D:KJ3803 4.1 47.5 1.0
CA D:LEU675 4.1 40.3 1.0
O D:HOH955 4.3 39.4 1.0
C D:SER677 4.3 40.2 1.0
CZ D:TYR524 4.7 48.9 1.0
CB D:VAL678 4.8 43.3 1.0
O8 D:KJ3803 4.8 55.1 1.0
CB D:LEU675 4.8 41.1 1.0
N D:CYS676 4.8 34.7 1.0
CA D:VAL678 4.9 41.8 1.0
O D:ASP674 4.9 38.0 1.0
O D:HOH962 5.0 47.9 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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