Fluorine in PDB 7k1f: Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558

Enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558

All present enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558:
3.4.24.56;

Protein crystallography data

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558, PDB code: 7k1f 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) 45.99 / 2.60
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 265.54, 265.54, 90.057, 90, 90, 120
R / Rfree (%) 17 / 20.8

Other elements in 7k1f:

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558 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_88558 (pdb code 7k1f). 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_88558, PDB code: 7k1f:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7k1f

Go back to Fluorine Binding Sites List in 7k1f
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558


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_88558 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:52.2
occ:1.00
 F27 A:VQJ1102 0.0 52.2 1.0
C26 A:VQJ1102 1.4 43.2 1.0
C28 A:VQJ1102 2.3 44.6 1.0
C25 A:VQJ1102 2.4 40.5 1.0
F29 A:VQJ1102 2.7 49.6 1.0
CA A:GLU817 3.1 37.8 1.0
CB A:GLU817 3.2 41.2 1.0
CG A:GLU817 3.3 40.8 1.0
C30 A:VQJ1102 3.6 44.4 1.0
C24 A:VQJ1102 3.6 45.9 1.0
N A:GLU817 3.8 41.3 1.0
C23 A:VQJ1102 4.1 44.4 1.0
CB A:SER132 4.3 41.0 1.0
OG A:SER816 4.3 40.9 1.0
C A:GLU817 4.3 37.1 1.0
C A:SER816 4.3 39.1 1.0
O A:SER816 4.4 35.8 1.0
CB A:PHE820 4.4 43.2 1.0
O A:GLU817 4.4 38.7 1.0
CB A:SER128 4.5 42.3 1.0
OG A:SER132 4.6 50.1 1.0
CD A:GLU817 4.6 47.0 1.0
O A:SER128 4.7 43.8 1.0
CG A:PHE820 4.9 45.9 1.0
CD2 A:PHE820 5.0 45.4 1.0
OE2 A:GLU817 5.0 47.2 1.0

Fluorine binding site 2 out of 4 in 7k1f

Go back to Fluorine Binding Sites List in 7k1f
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558


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_88558 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:49.6
occ:1.00
 F29 A:VQJ1102 0.0 49.6 1.0
C28 A:VQJ1102 1.3 44.6 1.0
C26 A:VQJ1102 2.3 43.2 1.0
C30 A:VQJ1102 2.4 44.4 1.0
F27 A:VQJ1102 2.7 52.2 1.0
CB A:SER128 3.2 42.3 1.0
OG A:SER128 3.2 45.7 1.0
CD2 A:PHE820 3.5 45.4 1.0
C23 A:VQJ1102 3.6 44.4 1.0
C25 A:VQJ1102 3.6 40.5 1.0
CE2 A:PHE820 4.0 48.0 1.0
C11 A:VQJ1102 4.0 37.3 1.0
C24 A:VQJ1102 4.1 45.9 1.0
CG A:PHE820 4.1 45.9 1.0
N10 A:VQJ1102 4.3 39.6 1.0
CA A:SER128 4.4 39.9 1.0
CB A:PHE820 4.5 43.2 1.0
CG A:GLU817 4.5 40.8 1.0
CZ A:PHE820 4.8 47.7 1.0
C22 A:VQJ1102 4.8 47.1 1.0
CD1 A:PHE820 4.9 46.1 1.0
C A:SER128 5.0 42.5 1.0

Fluorine binding site 3 out of 4 in 7k1f

Go back to Fluorine Binding Sites List in 7k1f
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558


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_88558 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:46.8
occ:1.00
 F27 B:VQJ1102 0.0 46.8 1.0
C26 B:VQJ1102 1.4 38.8 1.0
C25 B:VQJ1102 2.4 38.3 1.0
C28 B:VQJ1102 2.4 39.2 1.0
F29 B:VQJ1102 2.8 44.2 1.0
CA B:GLU817 3.0 37.5 1.0
CB B:GLU817 3.3 34.9 1.0
CG B:GLU817 3.4 41.0 1.0
O B:HOH1502 3.5 33.7 1.0
N B:GLU817 3.6 40.2 1.0
C24 B:VQJ1102 3.6 39.8 1.0
C30 B:VQJ1102 3.7 38.0 1.0
O B:HOH1321 3.9 30.5 1.0
C B:SER816 4.0 34.7 1.0
O B:SER816 4.0 34.8 1.0
OG B:SER132 4.1 42.1 1.0
OG B:SER816 4.1 35.5 1.0
C23 B:VQJ1102 4.1 39.5 1.0
C B:GLU817 4.2 38.5 1.0
CB B:SER132 4.3 32.7 1.0
CB B:PHE820 4.3 37.2 1.0
O B:GLU817 4.3 40.3 1.0
CD B:GLU817 4.7 43.5 1.0
CG B:PHE820 4.8 35.0 1.0
CD1 B:PHE820 5.0 36.5 1.0

Fluorine binding site 4 out of 4 in 7k1f

Go back to Fluorine Binding Sites List in 7k1f
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_88558


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_88558 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:44.2
occ:1.00
 F29 B:VQJ1102 0.0 44.2 1.0
C28 B:VQJ1102 1.4 39.2 1.0
C30 B:VQJ1102 2.4 38.0 1.0
C26 B:VQJ1102 2.4 38.8 1.0
F27 B:VQJ1102 2.8 46.8 1.0
OG B:SER128 3.3 37.0 1.0
O B:HOH1502 3.4 33.7 1.0
CB B:SER128 3.5 34.8 1.0
CD1 B:PHE820 3.5 36.5 1.0
O B:HOH1266 3.6 38.5 1.0
C23 B:VQJ1102 3.6 39.5 1.0
C25 B:VQJ1102 3.7 38.3 1.0
CE1 B:PHE820 3.9 37.7 1.0
C11 B:VQJ1102 3.9 41.5 1.0
CG B:PHE820 4.0 35.0 1.0
C24 B:VQJ1102 4.1 39.8 1.0
O B:HOH1454 4.2 33.7 1.0
N10 B:VQJ1102 4.4 39.7 1.0
CB B:PHE820 4.4 37.2 1.0
CG B:GLU817 4.4 41.0 1.0
CA B:SER128 4.6 34.5 1.0
CZ B:PHE820 4.7 40.5 1.0
CD2 B:PHE820 4.8 40.8 1.0
C22 B:VQJ1102 4.8 41.1 1.0
C12 B:VQJ1102 5.0 40.5 1.0
O B:HOH1260 5.0 42.4 1.0

Reference:

W.G.Liang, R.Deprez, D.Bosc, W.Tang. Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound 4 To Be Published.
Page generated: Fri Aug 2 08:10:10 2024

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