Fluorine in PDB 7k1d: Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291

Enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291

All present enzymatic activity of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291:
3.4.24.56;

Protein crystallography data

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291, PDB code: 7k1d 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) 45.42 / 3.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 264.313, 264.313, 90.468, 90, 90, 120
R / Rfree (%) 15.6 / 19.2

Other elements in 7k1d:

The structure of Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291 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_77291 (pdb code 7k1d). 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_77291, PDB code: 7k1d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7k1d

Go back to Fluorine Binding Sites List in 7k1d
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291


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_77291 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:70.5
occ:1.00
 F31 A:VQD1102 0.0 70.5 1.0
C30 A:VQD1102 1.4 57.1 1.0
C32 A:VQD1102 2.3 60.5 1.0
C29 A:VQD1102 2.4 59.2 1.0
F33 A:VQD1102 2.7 72.2 1.0
CA A:GLU817 3.1 62.8 1.0
CB A:GLU817 3.4 46.9 1.0
CG A:GLU817 3.5 51.9 1.0
C28 A:VQD1102 3.6 55.9 1.0
C34 A:VQD1102 3.6 58.3 1.0
N A:GLU817 3.7 61.9 1.0
OG A:SER816 4.0 50.6 1.0
O A:SER816 4.1 37.6 1.0
C A:SER816 4.1 53.3 1.0
C27 A:VQD1102 4.1 54.3 1.0
C A:GLU817 4.3 56.2 1.0
CB A:PHE820 4.4 44.6 1.0
CB A:SER132 4.4 54.5 1.0
O A:GLU817 4.5 49.6 1.0
OG A:SER132 4.6 63.3 1.0
CD A:GLU817 4.8 70.3 1.0
CG A:PHE820 5.0 49.6 1.0
O A:SER128 5.0 55.0 1.0
CB A:SER816 5.0 55.0 1.0

Fluorine binding site 2 out of 4 in 7k1d

Go back to Fluorine Binding Sites List in 7k1d
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291


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_77291 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:72.2
occ:1.00
 F33 A:VQD1102 0.0 72.2 1.0
C32 A:VQD1102 1.4 60.5 1.0
C30 A:VQD1102 2.3 57.1 1.0
C34 A:VQD1102 2.4 58.3 1.0
F31 A:VQD1102 2.7 70.5 1.0
CB A:SER128 3.4 56.5 1.0
CD2 A:PHE820 3.4 57.2 1.0
C29 A:VQD1102 3.6 59.2 1.0
C27 A:VQD1102 3.6 54.3 1.0
OG A:SER128 3.8 66.7 1.0
CG A:PHE820 4.0 49.6 1.0
CE2 A:PHE820 4.0 51.8 1.0
C28 A:VQD1102 4.1 55.9 1.0
CG A:GLU817 4.1 51.9 1.0
CB A:PHE820 4.2 44.6 1.0
C11 A:VQD1102 4.2 53.2 1.0
OE2 A:GLU817 4.5 74.0 1.0
CA A:SER128 4.5 51.9 1.0
C10 A:VQD1102 4.6 47.9 1.0
CA A:GLU817 4.9 62.8 1.0
CD A:GLU817 4.9 70.3 1.0
O A:SER128 4.9 55.0 1.0
CB A:GLU817 4.9 46.9 1.0
C A:SER128 4.9 52.5 1.0
CD1 A:PHE820 4.9 56.7 1.0
C26 A:VQD1102 5.0 60.7 1.0

Fluorine binding site 3 out of 4 in 7k1d

Go back to Fluorine Binding Sites List in 7k1d
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291


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_77291 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:76.1
occ:1.00
 F31 B:VQD1102 0.0 76.1 1.0
C30 B:VQD1102 1.4 58.1 1.0
C29 B:VQD1102 2.3 59.2 1.0
C32 B:VQD1102 2.4 49.0 1.0
F33 B:VQD1102 2.8 62.4 1.0
CA B:GLU817 2.9 40.0 1.0
CB B:GLU817 3.4 35.6 1.0
N B:GLU817 3.4 44.9 1.0
OG B:SER816 3.5 50.2 1.0
CG B:GLU817 3.6 42.2 1.0
C28 B:VQD1102 3.6 51.5 1.0
C34 B:VQD1102 3.7 46.6 1.0
C B:SER816 3.8 41.8 1.0
O B:SER816 3.9 34.6 1.0
C27 B:VQD1102 4.1 49.0 1.0
C B:GLU817 4.1 47.3 1.0
O B:GLU817 4.3 44.3 1.0
OG B:SER132 4.4 41.9 1.0
CB B:PHE820 4.4 44.8 1.0
CB B:SER816 4.6 54.7 1.0
CB B:SER132 4.6 36.5 1.0
CA B:SER816 4.8 43.6 1.0
CD B:GLU817 4.9 63.6 1.0

Fluorine binding site 4 out of 4 in 7k1d

Go back to Fluorine Binding Sites List in 7k1d
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound BDM_77291


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_77291 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1102

b:62.4
occ:1.00
 F33 B:VQD1102 0.0 62.4 1.0
C32 B:VQD1102 1.4 49.0 1.0
C34 B:VQD1102 2.4 46.6 1.0
C30 B:VQD1102 2.4 58.1 1.0
F31 B:VQD1102 2.8 76.1 1.0
OG B:SER128 3.2 60.2 1.0
CB B:SER128 3.5 46.0 1.0
C27 B:VQD1102 3.6 49.0 1.0
C29 B:VQD1102 3.7 59.2 1.0
CD1 B:PHE820 3.9 52.2 1.0
C28 B:VQD1102 4.1 51.5 1.0
CG B:GLU817 4.2 42.2 1.0
CG B:PHE820 4.2 45.2 1.0
C11 B:VQD1102 4.3 53.0 1.0
CB B:PHE820 4.4 44.8 1.0
CE1 B:PHE820 4.4 47.7 1.0
C10 B:VQD1102 4.5 53.7 1.0
CA B:SER128 4.6 43.6 1.0
OE2 B:GLU817 4.8 71.2 1.0
CA B:GLU817 4.8 40.0 1.0
CD2 B:PHE820 4.9 50.6 1.0
CB B:GLU817 4.9 35.6 1.0
C26 B:VQD1102 4.9 51.7 1.0
O B:SER128 5.0 44.0 1.0

Reference:

W.G.Liang, R.Deprez, D.Bosc, W.Tang. Crystal Structure of Human Insulin Degrading Enzyme (Ide) in Complex with Compound 2 To Be Published.
Page generated: Fri Sep 24 13:24:59 2021

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