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Fluorine in PDB 5sfq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq was solved by C.Joseph, J.U.Peters, 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) 43.26 / 2.21
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.458, 134.458, 234.587, 90, 90, 120
R / Rfree (%) 18.6 / 24.8

Other elements in 5sfq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide 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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide (pdb code 5sfq). 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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sfq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 1 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:36.7
occ:1.00
 F23 A:IO7803 0.0 36.7 1.0
C22 A:IO7803 1.4 39.5 1.0
F24 A:IO7803 2.1 50.0 1.0
C21 A:IO7803 2.5 34.0 1.0
N16 A:IO7803 3.0 33.5 1.0
N17 A:IO7803 3.0 36.1 1.0
CD1 A:PHE729 3.5 31.1 1.0
CA A:PHE729 3.7 26.3 1.0
CB A:PHE729 3.9 28.1 1.0
N A:PHE729 4.1 30.2 1.0
C20 A:IO7803 4.1 31.5 1.0
CG2 A:VAL733 4.2 28.9 1.0
C19 A:IO7803 4.2 32.7 1.0
CG A:PHE729 4.2 29.1 1.0
C A:GLY728 4.5 27.5 1.0
CE1 A:PHE729 4.6 33.1 1.0
O A:GLY728 4.7 29.2 1.0
C18 A:IO7803 4.8 31.0 1.0
C A:PHE729 4.9 27.9 1.0
CB A:ALA732 5.0 30.5 1.0

Fluorine binding site 2 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 2 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:50.0
occ:1.00
 F24 A:IO7803 0.0 50.0 1.0
C22 A:IO7803 1.4 39.5 1.0
F23 A:IO7803 2.1 36.7 1.0
C21 A:IO7803 2.4 34.0 1.0
N16 A:IO7803 2.9 33.5 1.0
N A:PHE729 3.3 30.2 1.0
C A:GLY728 3.6 27.5 1.0
C20 A:IO7803 3.6 31.5 1.0
O A:GLY725 3.7 32.2 1.0
CA A:PHE729 3.7 26.3 1.0
N17 A:IO7803 3.8 36.1 1.0
CA A:GLY728 3.9 26.9 1.0
CB A:PHE729 4.0 28.1 1.0
O A:GLY728 4.2 29.2 1.0
C18 A:IO7803 4.7 31.0 1.0
C19 A:IO7803 4.7 32.7 1.0
C A:GLY725 4.7 31.0 1.0
CD1 A:PHE729 4.8 31.1 1.0
N A:GLY728 4.8 30.8 1.0
CG A:PHE729 4.9 29.1 1.0

Fluorine binding site 3 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 3 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:36.7
occ:1.00
 F23 B:IO7803 0.0 36.7 1.0
C22 B:IO7803 1.4 37.9 1.0
F24 B:IO7803 2.2 48.5 1.0
C21 B:IO7803 2.5 34.1 1.0
N16 B:IO7803 3.0 32.5 1.0
N17 B:IO7803 3.0 30.4 1.0
CD1 B:PHE729 3.3 31.1 1.0
CA B:PHE729 3.5 29.6 1.0
CB B:PHE729 3.8 31.4 1.0
CG2 B:VAL733 3.9 31.1 1.0
CG B:PHE729 4.0 29.4 1.0
C20 B:IO7803 4.1 27.4 1.0
N B:PHE729 4.1 30.9 1.0
C19 B:IO7803 4.2 27.6 1.0
CE1 B:PHE729 4.3 30.6 1.0
O B:GLY728 4.4 33.2 1.0
C B:GLY728 4.5 31.1 1.0
C B:PHE729 4.7 27.3 1.0
O B:PHE729 4.7 27.1 1.0
C18 B:IO7803 4.8 27.6 1.0
CB B:ALA732 4.9 29.1 1.0
N14 B:IO7803 4.9 29.6 1.0

Fluorine binding site 4 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 4 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:48.5
occ:1.00
 F24 B:IO7803 0.0 48.5 1.0
C22 B:IO7803 1.4 37.9 1.0
F23 B:IO7803 2.2 36.7 1.0
C21 B:IO7803 2.4 34.1 1.0
N16 B:IO7803 3.0 32.5 1.0
N B:PHE729 3.3 30.9 1.0
C B:GLY728 3.4 31.1 1.0
CA B:PHE729 3.5 29.6 1.0
C20 B:IO7803 3.6 27.4 1.0
O B:GLY725 3.7 36.5 1.0
O B:GLY728 3.8 33.2 1.0
N17 B:IO7803 3.8 30.4 1.0
CB B:PHE729 3.9 31.4 1.0
CA B:GLY728 4.0 28.5 1.0
C18 B:IO7803 4.7 27.6 1.0
CD1 B:PHE729 4.7 31.1 1.0
C19 B:IO7803 4.7 27.6 1.0
CG B:PHE729 4.8 29.4 1.0
C B:GLY725 4.8 35.5 1.0
N B:GLY728 4.9 27.5 1.0
C B:PHE729 4.9 27.3 1.0

Fluorine binding site 5 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 5 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:49.0
occ:1.00
 F23 C:IO7803 0.0 49.0 1.0
C22 C:IO7803 1.4 52.1 1.0
F24 C:IO7803 2.2 60.6 1.0
C21 C:IO7803 2.4 50.4 1.0
N16 C:IO7803 3.0 36.6 1.0
N17 C:IO7803 3.2 37.2 1.0
CD1 C:PHE729 4.0 27.6 1.0
CA C:PHE729 4.0 33.4 1.0
C20 C:IO7803 4.1 34.7 1.0
CG2 C:VAL733 4.2 32.8 1.0
CB C:PHE729 4.3 33.1 1.0
C19 C:IO7803 4.4 33.3 1.0
N C:PHE729 4.5 44.9 1.0
O C:GLY728 4.6 42.1 1.0
CG C:PHE729 4.6 30.9 1.0
C C:GLY728 4.8 38.3 1.0
C18 C:IO7803 4.9 37.0 1.0
CE1 C:PHE729 4.9 27.4 1.0

Fluorine binding site 6 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 6 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:60.6
occ:1.00
 F24 C:IO7803 0.0 60.6 1.0
C22 C:IO7803 1.4 52.1 1.0
F23 C:IO7803 2.2 49.0 1.0
C21 C:IO7803 2.5 50.4 1.0
N16 C:IO7803 2.8 36.6 1.0
N C:PHE729 3.0 44.9 1.0
CA C:PHE729 3.1 33.4 1.0
C20 C:IO7803 3.1 34.7 1.0
CB C:PHE729 3.3 33.1 1.0
O C:GLY725 3.4 40.2 1.0
C C:GLY728 3.4 38.3 1.0
N17 C:IO7803 3.6 37.2 1.0
O C:GLY728 3.7 42.1 1.0
CA C:GLY728 4.1 38.5 1.0
C18 C:IO7803 4.2 37.0 1.0
CD1 C:PHE729 4.3 27.6 1.0
CG C:PHE729 4.3 30.9 1.0
C19 C:IO7803 4.3 33.3 1.0
C C:PHE729 4.5 34.9 1.0
C C:GLY725 4.5 42.2 1.0
N C:GLY728 4.9 39.7 1.0

Fluorine binding site 7 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 7 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:44.4
occ:1.00
 F23 D:IO7803 0.0 44.4 1.0
C22 D:IO7803 1.4 53.5 1.0
F24 D:IO7803 2.1 63.8 1.0
C21 D:IO7803 2.5 45.2 1.0
N16 D:IO7803 3.1 38.7 1.0
N17 D:IO7803 3.3 43.2 1.0
CD1 D:PHE729 3.9 27.3 1.0
CG2 D:VAL733 3.9 34.4 1.0
CA D:PHE729 4.1 33.7 1.0
C20 D:IO7803 4.3 32.6 1.0
CB D:PHE729 4.3 32.4 1.0
C19 D:IO7803 4.5 35.1 1.0
O D:GLY728 4.5 36.8 1.0
N D:PHE729 4.5 33.9 1.0
CG D:PHE729 4.6 28.2 1.0
C D:GLY728 4.7 34.8 1.0
CE1 D:PHE729 4.8 27.0 1.0
CB D:ALA732 4.9 31.5 1.0
C18 D:IO7803 5.0 32.8 1.0

Fluorine binding site 8 out of 8 in 5sfq

Go back to Fluorine Binding Sites List in 5sfq
Fluorine binding site 8 out of 8 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide


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 4- (Azetidine-1-Carbonyl)-N-[1-(2,2-Difluoroethyl)Pyrazol-3-Yl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:63.8
occ:1.00
 F24 D:IO7803 0.0 63.8 1.0
C22 D:IO7803 1.4 53.5 1.0
F23 D:IO7803 2.1 44.4 1.0
C21 D:IO7803 2.5 45.2 1.0
N16 D:IO7803 2.7 38.7 1.0
N D:PHE729 3.1 33.9 1.0
C20 D:IO7803 3.2 32.6 1.0
CA D:PHE729 3.3 33.7 1.0
O D:GLY725 3.3 35.9 1.0
C D:GLY728 3.4 34.8 1.0
N17 D:IO7803 3.5 43.2 1.0
CB D:PHE729 3.5 32.4 1.0
O D:GLY728 3.8 36.8 1.0
CA D:GLY728 4.1 34.0 1.0
C18 D:IO7803 4.2 32.8 1.0
C19 D:IO7803 4.3 35.1 1.0
CD1 D:PHE729 4.3 27.3 1.0
CG D:PHE729 4.4 28.2 1.0
C D:GLY725 4.5 36.1 1.0
C D:PHE729 4.7 32.6 1.0
N D:GLY728 5.0 34.4 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 14:15:49 2024

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