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Fluorine in PDB 5sfr: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfr was solved by C.Joseph, L.Gobbi, 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) 43.77 / 2.04
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.625, 135.625, 235.847, 90, 90, 120
R / Rfree (%) 18.1 / 21.3

Other elements in 5sfr:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide 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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide (pdb code 5sfr). 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 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfr:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5sfr

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Fluorine binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F803

b:54.3
occ:1.00
 F34 A:IOI803 0.0 54.3 1.0
C33 A:IOI803 1.4 50.4 1.0
C22 A:IOI803 2.5 39.0 1.0
O21 A:IOI803 2.9 47.6 1.0
CG A:PRO712 3.7 52.1 1.0
CB A:PRO712 3.8 50.5 1.0
C17 A:IOI803 4.2 38.7 1.0
CD A:LYS718 4.8 59.2 1.0
C16 A:IOI803 4.9 41.7 1.0
CG A:GLU721 5.0 59.9 1.0
CB A:GLU721 5.0 47.9 1.0

Fluorine binding site 2 out of 4 in 5sfr

Go back to Fluorine Binding Sites List in 5sfr
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F803

b:48.9
occ:1.00
 F34 B:IOI803 0.0 48.9 1.0
C33 B:IOI803 1.4 41.4 1.0
C22 B:IOI803 2.3 40.2 1.0
O21 B:IOI803 2.9 33.6 1.0
OE1 B:GLU721 3.2 74.8 1.0
CG B:PRO712 3.5 39.5 1.0
CB B:PRO712 3.8 40.3 1.0
C17 B:IOI803 4.2 35.2 1.0
CD B:GLU721 4.4 70.2 1.0
O B:HOH1061 4.6 40.3 1.0
C16 B:IOI803 4.9 32.8 1.0
CD B:PRO712 5.0 40.4 1.0

Fluorine binding site 3 out of 4 in 5sfr

Go back to Fluorine Binding Sites List in 5sfr
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F803

b:54.5
occ:1.00
 F34 C:IOI803 0.0 54.5 1.0
C33 C:IOI803 1.4 59.8 1.0
C22 C:IOI803 2.4 43.9 1.0
O21 C:IOI803 3.0 53.4 1.0
OE1 C:GLU721 3.5 73.7 1.0
CG C:PRO712 3.5 46.7 1.0
CB C:PRO712 3.8 48.1 1.0
CD C:GLU721 4.2 67.7 1.0
OE2 C:GLU721 4.2 63.4 1.0
C17 C:IOI803 4.2 42.6 1.0
CD C:LYS718 4.8 62.9 1.0
C16 C:IOI803 4.9 40.1 1.0

Fluorine binding site 4 out of 4 in 5sfr

Go back to Fluorine Binding Sites List in 5sfr
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide


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-N- Ethyl-3-N-[2-[3-(2-Fluoroethoxy)Phenyl]Imidazo[1,2-A]Pyrimidin-7-Yl]- 4-N,2-Dimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F803

b:67.3
occ:1.00
 F34 D:IOI803 0.0 67.3 1.0
C33 D:IOI803 1.4 52.3 1.0
C22 D:IOI803 2.4 43.8 1.0
O21 D:IOI803 3.0 47.3 1.0
CG D:PRO712 3.6 50.4 1.0
CB D:PRO712 3.8 49.4 1.0
C17 D:IOI803 4.3 40.5 1.0
OE2 D:GLU721 5.0 70.4 1.0
C16 D:IOI803 5.0 42.1 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 14:16:02 2024

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