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Fluorine in PDB 5siw: 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine

Enzymatic activity of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine

All present enzymatic activity of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5siw was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 2.13
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.88, 134.88, 235.159, 90, 90, 120
R / Rfree (%) 17 / 22.5

Other elements in 5siw:

The structure of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine also contains other interesting chemical elements:

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

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5siw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5siw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5siw

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Fluorine binding site 1 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:54.6
occ:1.00
 F25 A:JTX803 0.0 54.6 1.0
C24 A:JTX803 1.4 46.1 1.0
F26 A:JTX803 2.1 57.6 1.0
F27 A:JTX803 2.2 52.9 1.0
C3 A:JTX803 2.4 42.4 1.0
C2 A:JTX803 2.8 38.3 1.0
O A:HOH1013 3.2 45.4 1.0
O A:HOH962 3.3 47.8 1.0
C4 A:JTX803 3.7 39.4 1.0
CD2 A:LEU675 3.7 44.9 1.0
N1 A:JTX803 4.1 42.1 1.0
N8 A:JTX803 4.4 43.7 1.0
CD2 A:LEU635 4.7 45.8 1.0
O A:HOH979 4.7 45.2 1.0
N5 A:JTX803 4.8 40.5 1.0
CZ A:PHE729 4.8 36.1 1.0
C6 A:JTX803 4.9 41.0 1.0

Fluorine binding site 2 out of 12 in 5siw

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Fluorine binding site 2 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:57.6
occ:1.00
 F26 A:JTX803 0.0 57.6 1.0
C24 A:JTX803 1.3 46.1 1.0
F27 A:JTX803 1.9 52.9 1.0
F25 A:JTX803 2.1 54.6 1.0
C3 A:JTX803 2.5 42.4 1.0
C4 A:JTX803 3.2 39.4 1.0
CD2 A:LEU635 3.3 45.8 1.0
CE1 A:PHE729 3.4 42.6 1.0
N8 A:JTX803 3.5 43.7 1.0
C2 A:JTX803 3.5 38.3 1.0
CZ A:PHE729 3.7 36.1 1.0
O A:HOH1013 3.9 45.4 1.0
CD2 A:LEU675 4.1 44.9 1.0
N5 A:JTX803 4.5 40.5 1.0
CD1 A:PHE729 4.5 41.8 1.0
N1 A:JTX803 4.6 42.1 1.0
CG A:LEU635 4.7 44.8 1.0
C9 A:JTX803 4.8 34.8 1.0
CE2 A:PHE729 4.9 36.5 1.0

Fluorine binding site 3 out of 12 in 5siw

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Fluorine binding site 3 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:52.9
occ:1.00
 F27 A:JTX803 0.0 52.9 1.0
C24 A:JTX803 1.3 46.1 1.0
F26 A:JTX803 1.9 57.6 1.0
F25 A:JTX803 2.2 54.6 1.0
C3 A:JTX803 2.4 42.4 1.0
O A:HOH1013 2.8 45.4 1.0
C4 A:JTX803 2.9 39.4 1.0
N8 A:JTX803 2.9 43.7 1.0
CZ A:PHE696 3.3 39.7 1.0
C2 A:JTX803 3.6 38.3 1.0
CE2 A:PHE696 4.0 45.5 1.0
N5 A:JTX803 4.2 40.5 1.0
C9 A:JTX803 4.3 34.8 1.0
CE1 A:PHE696 4.4 40.5 1.0
N1 A:JTX803 4.7 42.1 1.0
CE1 A:PHE729 4.7 42.6 1.0
CD2 A:LEU635 4.9 45.8 1.0
N10 A:JTX803 4.9 37.8 1.0
C6 A:JTX803 4.9 41.0 1.0
CZ A:PHE729 5.0 36.1 1.0

Fluorine binding site 4 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 4 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:56.3
occ:1.00
 F25 B:JTX803 0.0 56.3 1.0
C24 B:JTX803 1.3 51.3 1.0
F27 B:JTX803 2.1 57.0 1.0
F26 B:JTX803 2.1 57.2 1.0
C3 B:JTX803 2.3 41.5 1.0
C2 B:JTX803 2.7 38.0 1.0
O B:HOH949 3.3 39.9 1.0
CD2 B:LEU675 3.4 35.8 1.0
C4 B:JTX803 3.6 41.0 1.0
O B:HOH1036 3.7 42.4 1.0
N1 B:JTX803 4.1 41.7 1.0
N8 B:JTX803 4.4 38.5 1.0
CZ B:PHE729 4.4 33.7 1.0
O B:HOH933 4.5 51.5 1.0
CD2 B:LEU635 4.6 39.3 1.0
N5 B:JTX803 4.7 43.1 1.0
CE1 B:PHE729 4.8 34.2 1.0
CG B:LEU675 4.9 36.6 1.0
C6 B:JTX803 4.9 44.4 1.0

Fluorine binding site 5 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 5 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:57.2
occ:1.00
 F26 B:JTX803 0.0 57.2 1.0
C24 B:JTX803 1.3 51.3 1.0
F27 B:JTX803 1.9 57.0 1.0
F25 B:JTX803 2.1 56.3 1.0
C3 B:JTX803 2.5 41.5 1.0
C4 B:JTX803 3.2 41.0 1.0
CD2 B:LEU635 3.3 39.3 1.0
CE1 B:PHE729 3.3 34.2 1.0
N8 B:JTX803 3.4 38.5 1.0
CZ B:PHE729 3.5 33.7 1.0
C2 B:JTX803 3.6 38.0 1.0
CD2 B:LEU675 4.2 35.8 1.0
O B:HOH1036 4.4 42.4 1.0
CD1 B:PHE729 4.5 36.3 1.0
N5 B:JTX803 4.6 43.1 1.0
CG B:LEU635 4.6 37.5 1.0
CE2 B:PHE729 4.7 33.1 1.0
C9 B:JTX803 4.7 40.8 1.0
N1 B:JTX803 4.8 41.7 1.0

Fluorine binding site 6 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 6 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:57.0
occ:1.00
 F27 B:JTX803 0.0 57.0 1.0
C24 B:JTX803 1.3 51.3 1.0
F26 B:JTX803 1.9 57.2 1.0
F25 B:JTX803 2.1 56.3 1.0
C3 B:JTX803 2.4 41.5 1.0
C4 B:JTX803 3.0 41.0 1.0
O B:HOH1036 3.0 42.4 1.0
N8 B:JTX803 3.1 38.5 1.0
CZ B:PHE696 3.5 39.1 1.0
C2 B:JTX803 3.5 38.0 1.0
CE2 B:PHE696 4.2 37.1 1.0
N5 B:JTX803 4.3 43.1 1.0
CE1 B:PHE696 4.4 37.1 1.0
C9 B:JTX803 4.4 40.8 1.0
N1 B:JTX803 4.7 41.7 1.0
CE1 B:PHE729 4.8 34.2 1.0
CZ B:PHE729 4.9 33.7 1.0
CD2 B:LEU635 4.9 39.3 1.0

Fluorine binding site 7 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 7 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:62.4
occ:1.00
 F25 C:JTX803 0.0 62.4 1.0
C24 C:JTX803 1.3 53.6 1.0
F26 C:JTX803 2.0 52.7 1.0
F27 C:JTX803 2.2 67.1 1.0
C3 C:JTX803 2.4 45.0 1.0
C2 C:JTX803 3.0 37.2 1.0
CD2 C:LEU675 3.5 36.5 1.0
C4 C:JTX803 3.7 42.9 1.0
O C:HOH1023 3.8 53.6 1.0
O C:HOH984 3.9 43.4 1.0
CD2 C:LEU635 4.0 54.6 1.0
O C:HOH1015 4.1 51.3 1.0
CZ C:PHE729 4.2 40.2 1.0
N8 C:JTX803 4.3 40.5 1.0
N1 C:JTX803 4.3 39.7 1.0
CE1 C:PHE729 4.5 41.1 1.0
N5 C:JTX803 4.8 44.0 1.0
CG C:LEU675 5.0 38.6 1.0
CG C:LEU635 5.0 43.1 1.0

Fluorine binding site 8 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 8 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:52.7
occ:1.00
 F26 C:JTX803 0.0 52.7 1.0
C24 C:JTX803 1.4 53.6 1.0
F25 C:JTX803 2.0 62.4 1.0
F27 C:JTX803 2.4 67.1 1.0
C3 C:JTX803 2.5 45.0 1.0
C4 C:JTX803 2.9 42.9 1.0
N8 C:JTX803 2.9 40.5 1.0
CE1 C:PHE729 3.4 41.1 1.0
C2 C:JTX803 3.7 37.2 1.0
CD2 C:LEU635 3.7 54.6 1.0
CZ C:PHE729 3.7 40.2 1.0
N5 C:JTX803 4.3 44.0 1.0
CD1 C:PHE729 4.3 39.7 1.0
C9 C:JTX803 4.3 47.9 1.0
O C:HOH1023 4.4 53.6 1.0
O C:HOH1033 4.5 61.0 1.0
CZ C:PHE696 4.7 39.2 1.0
CD2 C:LEU675 4.7 36.5 1.0
N1 C:JTX803 4.8 39.7 1.0
CE2 C:PHE729 4.8 46.2 1.0

Fluorine binding site 9 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 9 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:67.1
occ:1.00
 F27 C:JTX803 0.0 67.1 1.0
C24 C:JTX803 1.5 53.6 1.0
F25 C:JTX803 2.2 62.4 1.0
F26 C:JTX803 2.4 52.7 1.0
C3 C:JTX803 2.4 45.0 1.0
O C:HOH1023 2.7 53.6 1.0
C4 C:JTX803 3.1 42.9 1.0
C2 C:JTX803 3.2 37.2 1.0
CZ C:PHE696 3.4 39.2 1.0
N8 C:JTX803 3.5 40.5 1.0
CE2 C:PHE696 4.2 42.4 1.0
N5 C:JTX803 4.3 44.0 1.0
CE1 C:PHE696 4.3 39.6 1.0
N1 C:JTX803 4.4 39.7 1.0
O C:HOH984 4.5 43.4 1.0
C9 C:JTX803 4.7 47.9 1.0
CG2 C:ILE692 4.7 35.1 1.0
C6 C:JTX803 4.8 44.1 1.0
O C:HOH1015 4.9 51.3 1.0

Fluorine binding site 10 out of 12 in 5siw

Go back to Fluorine Binding Sites List in 5siw
Fluorine binding site 10 out of 12 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:67.4
occ:1.00
 F25 D:JTX803 0.0 67.4 1.0
C24 D:JTX803 1.3 60.2 1.0
F26 D:JTX803 2.1 77.2 1.0
F27 D:JTX803 2.2 71.6 1.0
C3 D:JTX803 2.3 52.1 1.0
C2 D:JTX803 2.7 48.8 1.0
C4 D:JTX803 3.6 48.4 1.0
CD2 D:LEU675 3.6 52.7 1.0
O D:HOH921 3.8 57.6 1.0
N1 D:JTX803 4.0 57.8 1.0
N8 D:JTX803 4.3 47.7 1.0
CZ D:PHE729 4.6 45.8 1.0
CD2 D:LEU635 4.6 55.9 1.0
N5 D:JTX803 4.7 52.5 1.0
CE1 D:PHE729 4.8 42.3 1.0
C6 D:JTX803 4.9 54.0 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 14:23:58 2024

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