Fluorine in PDB 6zqz: [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors

Enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors

All present enzymatic activity of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors:
3.1.4.17;

Protein crystallography data

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz was solved by G.Tresadern, P.M.Leonard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.07 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.960, 73.460, 92.230, 109.16, 91.37, 91.26
R / Rfree (%) 19.6 / 24.4

Other elements in 6zqz:

The structure of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors (pdb code 6zqz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors, PDB code: 6zqz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6zqz

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Fluorine binding site 1 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:19.0
occ:1.00
F24 A:QOQ1003 0.0 19.0 1.0
C23 A:QOQ1003 1.4 18.1 1.0
F25 A:QOQ1003 2.2 19.9 1.0
C18 A:QOQ1003 2.3 16.6 1.0
O A:LEU809 2.9 13.4 1.0
CA A:LEU809 3.0 12.1 1.0
N17 A:QOQ1003 3.0 16.0 1.0
C A:LEU809 3.2 12.6 1.0
C19 A:QOQ1003 3.3 15.9 1.0
CG A:GLN812 3.4 15.7 1.0
CB A:LEU809 3.4 12.2 1.0
CD2 A:LEU809 3.5 13.3 1.0
O A:HOH1195 3.7 14.9 1.0
CG A:LEU809 4.0 12.6 1.0
O A:ASP808 4.0 10.4 1.0
C16 A:QOQ1003 4.2 16.0 1.0
N A:LEU809 4.2 11.4 1.0
NE2 A:GLN812 4.2 16.1 1.0
N A:SER810 4.2 12.4 1.0
N A:GLN812 4.3 15.1 1.0
CB A:ASP811 4.3 15.1 1.0
CB A:GLN812 4.3 15.0 1.0
OH A:TYR655 4.4 13.8 1.0
CD A:GLN812 4.4 16.1 1.0
O A:HOH1194 4.4 15.4 1.0
N A:ASP811 4.5 13.8 1.0
C14 A:QOQ1003 4.5 15.9 1.0
CE2 A:PHE862 4.6 19.4 1.0
C A:ASP808 4.6 11.0 1.0
CZ A:PHE862 4.7 19.3 1.0
N15 A:QOQ1003 4.8 15.8 1.0
CA A:ASP811 4.8 14.6 1.0
CD1 A:LEU809 4.9 13.3 1.0
CA A:GLN812 4.9 15.2 1.0
C A:ASP811 4.9 15.2 1.0

Fluorine binding site 2 out of 8 in 6zqz

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Fluorine binding site 2 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:19.9
occ:1.00
F25 A:QOQ1003 0.0 19.9 1.0
C23 A:QOQ1003 1.4 18.1 1.0
F24 A:QOQ1003 2.2 19.0 1.0
C18 A:QOQ1003 2.3 16.6 1.0
N17 A:QOQ1003 2.7 16.0 1.0
CB A:ASP811 3.1 15.1 1.0
OH A:TYR655 3.3 13.8 1.0
CG2 A:ILE822 3.3 16.4 1.0
OD2 A:ASP811 3.5 15.7 1.0
C19 A:QOQ1003 3.5 15.9 1.0
O A:HOH1195 3.6 14.9 1.0
CG A:ASP811 3.8 15.7 1.0
NE2 A:GLN812 3.8 16.1 1.0
C16 A:QOQ1003 4.0 16.0 1.0
CG A:GLN812 4.0 15.7 1.0
CZ A:TYR655 4.1 13.4 1.0
CA A:ASP811 4.2 14.6 1.0
CE1 A:TYR655 4.2 13.4 1.0
O A:LEU809 4.3 13.4 1.0
CD A:GLN812 4.3 16.1 1.0
N A:GLN812 4.4 15.1 1.0
N A:ASP811 4.4 13.8 1.0
C A:ASP811 4.5 15.2 1.0
CB A:ILE822 4.5 16.7 1.0
C A:LEU809 4.6 12.6 1.0
C14 A:QOQ1003 4.7 15.9 1.0
CG1 A:ILE822 4.7 17.2 1.0
CA A:LEU809 4.7 12.1 1.0
N15 A:QOQ1003 4.8 15.8 1.0
O A:ASP808 4.9 10.4 1.0

Fluorine binding site 3 out of 8 in 6zqz

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Fluorine binding site 3 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:25.9
occ:1.00
F24 B:QOQ1003 0.0 25.9 1.0
C23 B:QOQ1003 1.4 24.3 1.0
F25 B:QOQ1003 2.2 27.9 1.0
C18 B:QOQ1003 2.3 22.6 1.0
N17 B:QOQ1003 2.9 22.2 1.0
CA B:LEU809 3.0 14.5 1.0
O B:LEU809 3.2 13.8 1.0
C B:LEU809 3.3 14.4 1.0
C19 B:QOQ1003 3.4 22.1 1.0
CB B:LEU809 3.5 14.7 1.0
CG B:GLN812 3.5 20.0 1.0
CD2 B:LEU809 3.5 15.8 1.0
O B:HOH1122 3.6 16.9 1.0
O B:ASP808 4.0 13.8 1.0
C16 B:QOQ1003 4.1 22.1 1.0
CG B:LEU809 4.1 14.9 1.0
NE2 B:GLN812 4.2 20.9 1.0
OH B:TYR655 4.2 16.4 1.0
N B:LEU809 4.3 13.8 1.0
N B:GLN812 4.3 19.0 1.0
N B:SER810 4.3 14.5 1.0
CB B:ASP811 4.4 18.1 1.0
CD B:GLN812 4.4 20.4 1.0
O B:HOH1217 4.4 19.9 1.0
CB B:GLN812 4.4 18.9 1.0
N B:ASP811 4.5 17.0 1.0
C14 B:QOQ1003 4.6 21.2 1.0
C B:ASP808 4.6 14.0 1.0
CE2 B:PHE862 4.6 21.2 1.0
CZ B:PHE862 4.7 20.9 1.0
N15 B:QOQ1003 4.8 22.4 1.0
CA B:ASP811 4.8 17.8 1.0
C B:ASP811 4.9 18.4 1.0
CA B:GLN812 5.0 18.6 1.0

Fluorine binding site 4 out of 8 in 6zqz

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Fluorine binding site 4 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:27.9
occ:1.00
F25 B:QOQ1003 0.0 27.9 1.0
C23 B:QOQ1003 1.4 24.3 1.0
F24 B:QOQ1003 2.2 25.9 1.0
C18 B:QOQ1003 2.2 22.6 1.0
N17 B:QOQ1003 2.7 22.2 1.0
OH B:TYR655 2.8 16.4 1.0
CG2 B:ILE822 3.3 21.3 1.0
C19 B:QOQ1003 3.4 22.1 1.0
CB B:ASP811 3.4 18.1 1.0
O B:HOH1122 3.4 16.9 1.0
OD2 B:ASP811 3.5 19.6 1.0
CZ B:TYR655 3.6 16.3 1.0
CE1 B:TYR655 3.9 16.4 1.0
CG B:ASP811 3.9 18.7 1.0
C16 B:QOQ1003 4.0 22.1 1.0
NE2 B:GLN812 4.1 20.9 1.0
C14 B:QOQ1003 4.5 21.2 1.0
CA B:ASP811 4.5 17.8 1.0
CB B:ILE822 4.6 21.9 1.0
CG B:GLN812 4.6 20.0 1.0
CE2 B:TYR655 4.6 15.7 1.0
O B:ASP808 4.6 13.8 1.0
N B:ASP811 4.7 17.0 1.0
N15 B:QOQ1003 4.7 22.4 1.0
O B:HOH1217 4.7 19.9 1.0
CG1 B:ILE822 4.7 21.8 1.0
CA B:LEU809 4.8 14.5 1.0
O B:LEU809 4.8 13.8 1.0
N B:GLN812 4.8 19.0 1.0
C B:LEU809 4.8 14.4 1.0
CD B:GLN812 4.8 20.4 1.0
C B:ASP811 4.9 18.4 1.0

Fluorine binding site 5 out of 8 in 6zqz

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Fluorine binding site 5 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:26.5
occ:1.00
F24 C:QOQ1003 0.0 26.5 1.0
C23 C:QOQ1003 1.3 25.2 1.0
F25 C:QOQ1003 2.2 28.1 1.0
C18 C:QOQ1003 2.3 23.8 1.0
N17 C:QOQ1003 2.8 22.9 1.0
O C:LEU809 3.1 17.1 1.0
CA C:LEU809 3.2 17.1 1.0
C C:LEU809 3.3 17.2 1.0
CG C:GLN812 3.4 20.4 1.0
C19 C:QOQ1003 3.4 21.8 1.0
CD2 C:LEU809 3.6 18.3 1.0
CB C:LEU809 3.7 17.5 1.0
O C:HOH1124 3.7 24.0 1.0
NE2 C:GLN812 4.0 20.8 1.0
C16 C:QOQ1003 4.0 22.8 1.0
O C:ASP808 4.0 15.4 1.0
N C:GLN812 4.1 19.8 1.0
CB C:ASP811 4.2 20.6 1.0
CD C:GLN812 4.2 21.0 1.0
OH C:TYR655 4.2 17.2 1.0
CG C:LEU809 4.2 17.8 1.0
CB C:GLN812 4.3 20.1 1.0
N C:LEU809 4.4 16.3 1.0
N C:ASP811 4.4 19.9 1.0
N C:SER810 4.4 17.6 1.0
C14 C:QOQ1003 4.5 21.7 1.0
O C:HOH1192 4.6 16.9 1.0
C C:ASP808 4.6 16.1 1.0
CA C:ASP811 4.7 20.1 1.0
N15 C:QOQ1003 4.7 22.1 1.0
CE2 C:PHE862 4.8 19.7 1.0
C C:ASP811 4.8 20.6 1.0
CA C:GLN812 4.9 19.9 1.0
OD2 C:ASP811 4.9 20.7 1.0

Fluorine binding site 6 out of 8 in 6zqz

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Fluorine binding site 6 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:28.1
occ:1.00
F25 C:QOQ1003 0.0 28.1 1.0
C23 C:QOQ1003 1.4 25.2 1.0
F24 C:QOQ1003 2.2 26.5 1.0
C18 C:QOQ1003 2.3 23.8 1.0
N17 C:QOQ1003 2.8 22.9 1.0
OH C:TYR655 2.8 17.2 1.0
CB C:ASP811 3.2 20.6 1.0
OD2 C:ASP811 3.2 20.7 1.0
CG2 C:ILE822 3.3 21.7 1.0
C19 C:QOQ1003 3.4 21.8 1.0
O C:HOH1124 3.5 24.0 1.0
CZ C:TYR655 3.6 16.5 1.0
CG C:ASP811 3.6 20.3 1.0
CE1 C:TYR655 3.9 16.6 1.0
NE2 C:GLN812 4.0 20.8 1.0
C16 C:QOQ1003 4.1 22.8 1.0
CA C:ASP811 4.3 20.1 1.0
CB C:ILE822 4.4 21.6 1.0
CG1 C:ILE822 4.4 22.3 1.0
CG C:GLN812 4.5 20.4 1.0
N C:ASP811 4.5 19.9 1.0
C14 C:QOQ1003 4.6 21.7 1.0
O C:ASP808 4.6 15.4 1.0
N C:GLN812 4.6 19.8 1.0
CD C:GLN812 4.7 21.0 1.0
O C:LEU809 4.7 17.1 1.0
CE2 C:TYR655 4.7 16.1 1.0
N15 C:QOQ1003 4.8 22.1 1.0
O C:HOH1192 4.8 16.9 1.0
C C:ASP811 4.8 20.6 1.0
C C:LEU809 4.9 17.2 1.0
CA C:LEU809 4.9 17.1 1.0
OD1 C:ASP811 4.9 20.3 1.0

Fluorine binding site 7 out of 8 in 6zqz

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Fluorine binding site 7 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1003

b:25.0
occ:1.00
F24 D:QOQ1003 0.0 25.0 1.0
C23 D:QOQ1003 1.4 24.0 1.0
F25 D:QOQ1003 2.2 28.7 1.0
C18 D:QOQ1003 2.4 22.3 1.0
N17 D:QOQ1003 2.9 21.3 1.0
O D:LEU809 2.9 12.3 1.0
CA D:LEU809 3.0 13.8 1.0
C D:LEU809 3.2 13.4 1.0
CG D:GLN812 3.4 16.6 1.0
C19 D:QOQ1003 3.5 21.4 1.0
O D:HOH1142 3.5 18.1 1.0
CB D:LEU809 3.5 14.1 1.0
CD2 D:LEU809 3.6 14.7 1.0
N D:GLN812 4.0 15.7 1.0
O D:ASP808 4.0 12.1 1.0
CB D:ASP811 4.1 17.7 1.0
C16 D:QOQ1003 4.2 21.6 1.0
NE2 D:GLN812 4.2 17.4 1.0
CG D:LEU809 4.2 14.3 1.0
OH D:TYR655 4.2 18.1 1.0
N D:LEU809 4.2 13.3 1.0
N D:SER810 4.2 14.0 1.0
CB D:GLN812 4.3 16.1 1.0
N D:ASP811 4.3 16.0 1.0
CD D:GLN812 4.3 16.8 1.0
C D:ASP808 4.6 12.8 1.0
CA D:ASP811 4.6 16.6 1.0
C14 D:QOQ1003 4.6 20.9 1.0
C D:ASP811 4.7 16.5 1.0
O D:HOH1278 4.7 16.9 1.0
CA D:GLN812 4.8 15.5 1.0
CE2 D:PHE862 4.8 19.9 1.0
N15 D:QOQ1003 4.8 21.7 1.0
OD2 D:ASP811 4.9 20.2 1.0

Fluorine binding site 8 out of 8 in 6zqz

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Fluorine binding site 8 out of 8 in the [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of [1,2,4]Triazolo[1,5-A]Pyrimidine Phosphodiesterase 2 Inhibitors within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1003

b:28.7
occ:1.00
F25 D:QOQ1003 0.0 28.7 1.0
C23 D:QOQ1003 1.4 24.0 1.0
F24 D:QOQ1003 2.2 25.0 1.0
C18 D:QOQ1003 2.3 22.3 1.0
OH D:TYR655 2.7 18.1 1.0
N17 D:QOQ1003 2.8 21.3 1.0
CB D:ASP811 3.2 17.7 1.0
O D:HOH1142 3.2 18.1 1.0
OD2 D:ASP811 3.2 20.2 1.0
C19 D:QOQ1003 3.4 21.4 1.0
CG2 D:ILE822 3.4 21.2 1.0
CZ D:TYR655 3.5 17.3 1.0
CG D:ASP811 3.7 18.5 1.0
CE1 D:TYR655 3.8 17.2 1.0
C16 D:QOQ1003 4.1 21.6 1.0
NE2 D:GLN812 4.2 17.4 1.0
CA D:ASP811 4.3 16.6 1.0
N D:ASP811 4.5 16.0 1.0
CG D:GLN812 4.5 16.6 1.0
C14 D:QOQ1003 4.5 20.9 1.0
O D:ASP808 4.5 12.1 1.0
CB D:ILE822 4.6 21.0 1.0
O D:LEU809 4.6 12.3 1.0
CE2 D:TYR655 4.6 17.0 1.0
N D:GLN812 4.7 15.7 1.0
CA D:LEU809 4.7 13.8 1.0
N15 D:QOQ1003 4.7 21.7 1.0
C D:LEU809 4.7 13.4 1.0
C D:ASP811 4.8 16.5 1.0
CD D:GLN812 4.8 16.8 1.0
CG1 D:ILE822 4.8 21.1 1.0
O D:HOH1278 4.9 16.9 1.0
OD1 D:ASP811 4.9 18.8 1.0

Reference:

G.Tresadern, I.Velter, A.A.Trabanco, F.Van Den Keybus, G.J.Macdonald, M.V.F.Somers, G.Vanhoof, P.M.Leonard, M.B.A.C.Lamers, Y.E.M.Van Roosbroeck, P.J.J.A.Buijnsters. [1,2,4]Triazolo[1,5- A ]Pyrimidine Phosphodiesterase 2A Inhibitors: Structure and Free-Energy Perturbation-Guided Exploration. J.Med.Chem. V. 63 12887 2020.
ISSN: ISSN 0022-2623
PubMed: 33105987
DOI: 10.1021/ACS.JMEDCHEM.0C01272
Page generated: Sun Dec 13 13:46:34 2020

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