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Fluorine in PDB 5sfk: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfk was solved by C.Joseph, R.M.Rodriguez-Sarmiento, 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) 43.48 / 2.33
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.55, 135.55, 233.95, 90, 90, 120
R / Rfree (%) 18.5 / 24.8

Other elements in 5sfk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide also contains other interesting chemical elements:

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

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide (pdb code 5sfk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide, PDB code: 5sfk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 5sfk

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:55.2
occ:1.00
 F25 A:IL6803 0.0 55.2 1.0
C10 A:IL6803 1.4 48.8 1.0
F27 A:IL6803 2.3 49.5 1.0
F26 A:IL6803 2.3 46.9 1.0
C12 A:IL6803 2.3 50.1 1.0
N6 A:IL6803 2.8 42.6 1.0
N A:PHE729 3.1 34.2 1.0
C A:GLY728 3.3 31.2 1.0
CA A:PHE729 3.4 32.2 1.0
C14 A:IL6803 3.4 41.8 1.0
N4 A:IL6803 3.6 41.8 1.0
O A:GLY725 3.6 41.7 1.0
O A:GLY728 3.7 33.0 1.0
CA A:GLY728 3.8 33.7 1.0
CB A:PHE729 3.8 32.6 1.0
C8 A:IL6803 4.4 41.6 1.0
C5 A:IL6803 4.4 39.7 1.0
CD1 A:PHE729 4.6 35.1 1.0
CG A:PHE729 4.8 32.5 1.0
C A:PHE729 4.8 30.7 1.0
C A:GLY725 4.8 36.9 1.0
N A:GLY728 4.9 35.0 1.0

Fluorine binding site 2 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 2 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:46.9
occ:1.00
 F26 A:IL6803 0.0 46.9 1.0
C10 A:IL6803 1.4 48.8 1.0
F27 A:IL6803 2.1 49.5 1.0
F25 A:IL6803 2.3 55.2 1.0
C12 A:IL6803 2.4 50.1 1.0
N6 A:IL6803 3.7 42.6 1.0
N4 A:IL6803 4.4 41.8 1.0
C14 A:IL6803 4.8 41.8 1.0

Fluorine binding site 3 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 3 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:49.5
occ:1.00
 F27 A:IL6803 0.0 49.5 1.0
C10 A:IL6803 1.4 48.8 1.0
F26 A:IL6803 2.1 46.9 1.0
F25 A:IL6803 2.3 55.2 1.0
C12 A:IL6803 2.4 50.1 1.0
N6 A:IL6803 2.9 42.6 1.0
N4 A:IL6803 2.9 41.8 1.0
CD1 A:PHE729 3.9 35.1 1.0
C5 A:IL6803 4.1 39.7 1.0
C14 A:IL6803 4.1 41.8 1.0
CG2 A:VAL733 4.1 36.6 1.0
CA A:PHE729 4.2 32.2 1.0
CB A:PHE729 4.5 32.6 1.0
CG A:PHE729 4.7 32.5 1.0
N A:PHE729 4.7 34.2 1.0
C8 A:IL6803 4.7 41.6 1.0
CE1 A:PHE729 4.7 39.8 1.0
O A:GLY728 4.9 33.0 1.0
N7 A:IL6803 5.0 38.1 1.0
C A:GLY728 5.0 31.2 1.0

Fluorine binding site 4 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 4 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:55.4
occ:1.00
 F25 B:IL6803 0.0 55.4 1.0
C10 B:IL6803 1.4 53.9 1.0
F27 B:IL6803 2.3 49.0 1.0
F26 B:IL6803 2.4 55.2 1.0
C12 B:IL6803 2.4 53.9 1.0
N6 B:IL6803 2.8 51.3 1.0
C14 B:IL6803 3.1 49.8 1.0
O B:GLY725 3.4 41.6 1.0
N B:PHE729 3.6 35.8 1.0
C B:GLY728 3.7 38.8 1.0
CA B:GLY728 3.8 37.4 1.0
N4 B:IL6803 4.0 55.2 1.0
CA B:PHE729 4.1 36.1 1.0
C8 B:IL6803 4.2 46.4 1.0
O B:GLY728 4.4 38.3 1.0
C B:GLY725 4.4 44.2 1.0
CB B:PHE729 4.4 34.5 1.0
C5 B:IL6803 4.7 43.0 1.0
CA B:GLY725 4.7 44.0 1.0
N B:GLY728 4.8 38.2 1.0

Fluorine binding site 5 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 5 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:55.2
occ:1.00
 F26 B:IL6803 0.0 55.2 1.0
C10 B:IL6803 1.4 53.9 1.0
F27 B:IL6803 2.2 49.0 1.0
C12 B:IL6803 2.3 53.9 1.0
F25 B:IL6803 2.4 55.4 1.0
N6 B:IL6803 3.6 51.3 1.0
N4 B:IL6803 4.5 55.2 1.0
C14 B:IL6803 4.5 49.8 1.0
C B:GLY728 5.0 38.8 1.0

Fluorine binding site 6 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 6 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:49.0
occ:1.00
 F27 B:IL6803 0.0 49.0 1.0
C10 B:IL6803 1.4 53.9 1.0
F26 B:IL6803 2.2 55.2 1.0
F25 B:IL6803 2.3 55.4 1.0
C12 B:IL6803 2.4 53.9 1.0
N6 B:IL6803 2.8 51.3 1.0
N4 B:IL6803 3.3 55.2 1.0
CA B:PHE729 3.4 36.1 1.0
CD1 B:PHE729 3.6 34.5 1.0
C14 B:IL6803 3.7 49.8 1.0
N B:PHE729 3.8 35.8 1.0
CB B:PHE729 3.9 34.5 1.0
C B:GLY728 4.0 38.8 1.0
O B:GLY728 4.1 38.3 1.0
CG B:PHE729 4.2 34.0 1.0
C5 B:IL6803 4.2 43.0 1.0
CG2 B:VAL733 4.2 36.2 1.0
C8 B:IL6803 4.5 46.4 1.0
CE1 B:PHE729 4.6 35.5 1.0
C B:PHE729 4.6 35.1 1.0
CB B:ALA732 4.7 36.0 1.0
O B:PHE729 4.7 34.2 1.0
CA B:GLY728 4.9 37.4 1.0
O B:GLY725 4.9 41.6 1.0

Fluorine binding site 7 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 7 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:60.3
occ:1.00
 F25 C:IL6803 0.0 60.3 1.0
C10 C:IL6803 1.4 56.7 1.0
F26 C:IL6803 2.3 59.7 1.0
F27 C:IL6803 2.4 50.3 1.0
C12 C:IL6803 2.4 55.9 1.0
N6 C:IL6803 2.8 52.5 1.0
N C:PHE729 3.1 43.0 1.0
C14 C:IL6803 3.3 51.6 1.0
CA C:PHE729 3.3 40.5 1.0
C C:GLY728 3.3 44.6 1.0
O C:GLY725 3.4 46.0 1.0
CB C:PHE729 3.7 41.6 1.0
N4 C:IL6803 3.7 56.4 1.0
O C:GLY728 3.7 43.9 1.0
CA C:GLY728 4.0 40.5 1.0
C8 C:IL6803 4.3 49.9 1.0
C5 C:IL6803 4.5 49.5 1.0
C C:GLY725 4.5 44.5 1.0
CD1 C:PHE729 4.6 42.8 1.0
CG C:PHE729 4.7 43.0 1.0
C C:PHE729 4.7 38.9 1.0
N C:GLY728 4.8 37.4 1.0

Fluorine binding site 8 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 8 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:59.7
occ:1.00
 F26 C:IL6803 0.0 59.7 1.0
C10 C:IL6803 1.4 56.7 1.0
F27 C:IL6803 2.2 50.3 1.0
F25 C:IL6803 2.3 60.3 1.0
C12 C:IL6803 2.5 55.9 1.0
N6 C:IL6803 3.8 52.5 1.0
N4 C:IL6803 4.6 56.4 1.0
O C:GLY728 4.7 43.9 1.0
C14 C:IL6803 4.7 51.6 1.0
C C:GLY728 4.8 44.6 1.0
N C:PHE729 5.0 43.0 1.0

Fluorine binding site 9 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 9 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:50.3
occ:1.00
 F27 C:IL6803 0.0 50.3 1.0
C10 C:IL6803 1.4 56.7 1.0
F26 C:IL6803 2.2 59.7 1.0
F25 C:IL6803 2.4 60.3 1.0
C12 C:IL6803 2.4 55.9 1.0
N6 C:IL6803 2.9 52.5 1.0
N4 C:IL6803 3.1 56.4 1.0
CD1 C:PHE729 3.9 42.8 1.0
CG2 C:VAL733 4.0 40.9 1.0
CA C:PHE729 4.0 40.5 1.0
C14 C:IL6803 4.1 51.6 1.0
C5 C:IL6803 4.3 49.5 1.0
CB C:PHE729 4.3 41.6 1.0
N C:PHE729 4.5 43.0 1.0
CG C:PHE729 4.6 43.0 1.0
O C:GLY728 4.7 43.9 1.0
C8 C:IL6803 4.8 49.9 1.0
CE1 C:PHE729 4.8 42.6 1.0
C C:GLY728 4.8 44.6 1.0

Fluorine binding site 10 out of 12 in 5sfk

Go back to Fluorine Binding Sites List in 5sfk
Fluorine binding site 10 out of 12 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)-N-[1-(2,2,2-Trifluoroethyl) Pyrazol-3-Yl]Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:91.3
occ:1.00
 F25 D:IL6803 0.0 91.3 1.0
C10 D:IL6803 1.4 86.4 1.0
C12 D:IL6803 2.3 76.6 1.0
F26 D:IL6803 2.3 84.0 1.0
F27 D:IL6803 2.3 74.3 1.0
N6 D:IL6803 3.0 72.2 1.0
C D:GLY728 3.5 64.1 1.0
N D:PHE729 3.5 68.8 1.0
O D:GLY725 3.6 67.1 1.0
C14 D:IL6803 3.8 67.5 1.0
CA D:GLY728 3.8 68.4 1.0
O D:GLY728 3.8 66.4 1.0
N4 D:IL6803 3.9 67.8 1.0
CA D:PHE729 3.9 68.8 1.0
CB D:PHE729 4.2 63.1 1.0
C D:GLY725 4.7 71.0 1.0
C8 D:IL6803 4.8 62.2 1.0
C5 D:IL6803 4.9 62.2 1.0
N D:GLY728 4.9 69.5 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 14:15:43 2024

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