Atomistry » Fluorine » PDB 5sb0-5sjo » 5sfr
Atomistry »
  Fluorine »
    PDB 5sb0-5sjo »
      5sfr »

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

Go back to Fluorine Binding Sites List in 5sfr
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: Tue Apr 4 23:42:09 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy