Fluorine in PDB 7k1e: Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646

Enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646

All present enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646:
3.4.24.56;

Protein crystallography data

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646, PDB code: 7k1e was solved by W.G.Liang, R.Deprez, D.Bosc, W.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.84 / 2.80
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 267.88, 267.88, 89.611, 90, 90, 120
R / Rfree (%) 15.8 / 20.9

Other elements in 7k1e:

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 (pdb code 7k1e). 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 Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646, PDB code: 7k1e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7k1e

Go back to Fluorine Binding Sites List in 7k1e
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646


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 Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:62.1
occ:1.00
 F27 A:VQG1102 0.0 62.1 1.0
C26 A:VQG1102 1.4 42.3 1.0
C25 A:VQG1102 2.4 31.1 1.0
C28 A:VQG1102 2.4 35.0 1.0
F29 A:VQG1102 2.9 64.6 1.0
CA A:GLU817 3.3 32.8 1.0
CG A:GLU817 3.3 47.3 1.0
CB A:GLU817 3.3 45.4 1.0
C24 A:VQG1102 3.6 33.0 1.0
C30 A:VQG1102 3.7 39.8 1.0
N A:GLU817 3.9 46.0 1.0
CB A:SER132 4.1 36.4 1.0
C23 A:VQG1102 4.1 49.7 1.0
OG A:SER132 4.2 66.4 1.0
OG A:SER816 4.4 36.9 1.0
C A:SER816 4.4 37.3 1.0
C A:GLU817 4.5 40.7 1.0
O A:SER816 4.5 33.9 1.0
CB A:PHE820 4.5 31.3 1.0
CB A:SER128 4.6 38.2 1.0
O A:GLU817 4.6 39.1 1.0
CD A:GLU817 4.7 58.3 1.0
O A:SER128 4.7 40.0 1.0
OE2 A:GLU817 5.0 53.3 1.0
CG A:PHE820 5.0 45.7 1.0

Fluorine binding site 2 out of 4 in 7k1e

Go back to Fluorine Binding Sites List in 7k1e
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646


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 Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:64.6
occ:1.00
 F29 A:VQG1102 0.0 64.6 1.0
C28 A:VQG1102 1.4 35.0 1.0
C30 A:VQG1102 2.3 39.8 1.0
C26 A:VQG1102 2.4 42.3 1.0
F27 A:VQG1102 2.9 62.1 1.0
CB A:SER128 3.2 38.2 1.0
OG A:SER128 3.3 42.2 1.0
CD2 A:PHE820 3.5 46.5 1.0
C23 A:VQG1102 3.6 49.7 1.0
C25 A:VQG1102 3.6 31.1 1.0
CE2 A:PHE820 3.9 42.7 1.0
C11 A:VQG1102 3.9 41.8 1.0
C10 A:VQG1102 3.9 37.0 1.0
C24 A:VQG1102 4.1 33.0 1.0
CG A:PHE820 4.1 45.7 1.0
CA A:SER128 4.5 35.2 1.0
CB A:PHE820 4.5 31.3 1.0
CG A:GLU817 4.6 47.3 1.0
CZ A:PHE820 4.8 48.8 1.0
C22 A:VQG1102 4.8 43.5 1.0
C12 A:VQG1102 5.0 33.8 1.0

Fluorine binding site 3 out of 4 in 7k1e

Go back to Fluorine Binding Sites List in 7k1e
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646


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 Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:51.3
occ:1.00
 F27 B:VQG1102 0.0 51.3 1.0
C26 B:VQG1102 1.4 38.9 1.0
C25 B:VQG1102 2.4 35.2 1.0
C28 B:VQG1102 2.4 35.4 1.0
F29 B:VQG1102 2.8 41.0 1.0
CA B:GLU817 3.0 31.5 1.0
CB B:GLU817 3.2 24.5 1.0
CG B:GLU817 3.3 42.1 1.0
N B:GLU817 3.6 31.2 1.0
C24 B:VQG1102 3.6 28.2 1.0
C30 B:VQG1102 3.6 42.1 1.0
O B:HOH1337 3.7 30.5 1.0
OG B:SER132 3.9 45.4 1.0
C23 B:VQG1102 4.1 39.0 1.0
O B:HOH1218 4.1 22.0 1.0
C B:SER816 4.1 28.4 1.0
O B:SER816 4.2 35.0 1.0
CB B:SER132 4.2 22.7 1.0
OG B:SER816 4.2 30.1 1.0
C B:GLU817 4.3 39.7 1.0
CB B:PHE820 4.3 31.1 1.0
O B:HOH1307 4.4 37.3 1.0
O B:GLU817 4.4 35.2 1.0
CD B:GLU817 4.7 45.7 1.0
CG B:PHE820 4.7 27.3 1.0
CD2 B:PHE820 4.9 44.1 1.0
CB B:SER128 5.0 25.5 1.0

Fluorine binding site 4 out of 4 in 7k1e

Go back to Fluorine Binding Sites List in 7k1e
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646


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 Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88646 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:41.0
occ:1.00
 F29 B:VQG1102 0.0 41.0 1.0
C28 B:VQG1102 1.3 35.4 1.0
C30 B:VQG1102 2.3 42.1 1.0
C26 B:VQG1102 2.4 38.9 1.0
F27 B:VQG1102 2.8 51.3 1.0
O B:HOH1307 3.0 37.3 1.0
OG B:SER128 3.3 34.2 1.0
CB B:SER128 3.4 25.5 1.0
O B:HOH1337 3.4 30.5 1.0
CD2 B:PHE820 3.6 44.1 1.0
C23 B:VQG1102 3.6 39.0 1.0
C25 B:VQG1102 3.7 35.2 1.0
CE2 B:PHE820 3.9 36.0 1.0
C10 B:VQG1102 4.0 27.7 1.0
CG B:PHE820 4.1 27.3 1.0
C24 B:VQG1102 4.1 28.2 1.0
C11 B:VQG1102 4.1 40.0 1.0
CA B:SER128 4.5 30.2 1.0
CB B:PHE820 4.5 31.1 1.0
CG B:GLU817 4.5 42.1 1.0
CZ B:PHE820 4.8 36.8 1.0
C22 B:VQG1102 4.8 34.0 1.0
CD1 B:PHE820 4.9 33.1 1.0
N21 B:VQG1102 5.0 25.1 1.0
C B:SER128 5.0 26.0 1.0
O B:HOH1246 5.0 28.0 1.0

Reference:

W.G.Liang, R.Deprez, D.Bosc, W.Tang. Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound 3 To Be Published.
Page generated: Fri Aug 2 08:09:51 2024

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