Fluorine in PDB 6byz: Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37

Enzymatic activity of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37

All present enzymatic activity of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37:
3.4.24.56;

Protein crystallography data

The structure of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37, PDB code: 6byz was solved by G.A.Tan, M.A.Seeliger, J.P.Maianti, D.R.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.48 / 2.96
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 264.486, 264.486, 91.094, 90.00, 90.00, 120.00
R / Rfree (%) 16.1 / 20.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 (pdb code 6byz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37, PDB code: 6byz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6byz

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Fluorine binding site 1 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.1
occ:0.79
 F01 A:J181101 0.0 0.1 0.8
C09 A:J181101 1.4 0.0 0.8
H10 A:J181101 2.1 90.7 0.8
F03 A:J181101 2.2 0.8 0.8
F02 A:J181101 2.2 0.8 0.8
C08 A:J181101 2.3 86.2 0.8
C10 A:J181101 2.5 75.6 0.8
CA D:ALA3 2.9 94.4 1.0
C A:GLY361 3.3 45.5 1.0
O A:GLY361 3.3 53.1 1.0
N D:ALA3 3.4 93.9 1.0
CB D:ALA3 3.5 92.0 1.0
N A:GLY362 3.6 45.9 1.0
C07 A:J181101 3.6 77.2 0.8
CA A:GLY361 3.8 43.7 1.0
N A:GLY361 3.9 45.0 1.0
C11 A:J181101 3.9 69.6 0.8
CA A:GLY362 4.0 44.3 1.0
C D:ALA3 4.0 92.7 1.0
C D:ALA2 4.1 83.5 1.0
C A:GLY362 4.2 40.8 1.0
O A:GLY362 4.3 31.4 1.0
CG2 A:ILE374 4.4 35.3 1.0
O D:ALA2 4.4 75.6 1.0
H11 A:J181101 4.5 83.5 0.8
CG2 A:VAL360 4.5 36.8 1.0
C A:VAL360 4.5 45.6 1.0
O A:GLN363 4.7 40.4 1.0
C13 A:J181101 4.7 68.3 0.8
O D:ALA3 4.7 89.0 1.0
CB A:VAL360 4.7 38.4 1.0
S01 A:J181101 4.7 81.8 0.8
O02 A:J181101 4.8 77.7 0.8
C12 A:J181101 4.8 67.5 0.8
N A:GLN363 4.9 39.2 1.0
O D:ALA1 5.0 79.1 1.0
O D:HOH101 5.0 62.0 1.0
O A:ILE374 5.0 41.6 1.0
O03 A:J181101 5.0 83.3 0.8
O A:VAL360 5.0 45.6 1.0

Fluorine binding site 2 out of 6 in 6byz

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Fluorine binding site 2 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.8
occ:0.79
 F02 A:J181101 0.0 0.8 0.8
C09 A:J181101 1.3 0.0 0.8
F03 A:J181101 2.2 0.8 0.8
F01 A:J181101 2.2 0.1 0.8
C08 A:J181101 2.3 86.2 0.8
C07 A:J181101 2.9 77.2 0.8
CG2 A:ILE374 2.9 35.3 1.0
O03 A:J181101 3.0 83.3 0.8
S01 A:J181101 3.2 81.8 0.8
C10 A:J181101 3.4 75.6 0.8
CG2 A:VAL360 3.4 36.8 1.0
O02 A:J181101 3.5 77.7 0.8
H10 A:J181101 3.6 90.7 0.8
CA A:GLY361 3.9 43.7 1.0
O A:VAL360 3.9 45.6 1.0
N A:GLY361 3.9 45.0 1.0
C A:VAL360 3.9 45.6 1.0
C A:GLY361 4.1 45.5 1.0
O A:ILE374 4.2 41.6 1.0
C13 A:J181101 4.2 68.3 0.8
CB A:VAL360 4.2 38.4 1.0
N A:GLY362 4.3 45.9 1.0
CB A:ILE374 4.4 48.3 1.0
C11 A:J181101 4.5 69.6 0.8
C A:ILE374 4.6 44.8 1.0
O A:GLY361 4.6 53.1 1.0
N02 A:J181101 4.7 79.0 0.8
CA A:VAL360 4.8 41.1 1.0
CB A:ASN376 4.8 75.0 1.0
O A:GLY362 4.8 31.4 1.0
C12 A:J181101 4.9 67.5 0.8
O A:HOH1382 4.9 78.5 1.0
H13 A:J181101 4.9 82.0 0.8
H31 A:J181101 5.0 89.6 0.8

Fluorine binding site 3 out of 6 in 6byz

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Fluorine binding site 3 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1101

b:0.8
occ:0.79
 F03 A:J181101 0.0 0.8 0.8
C09 A:J181101 1.3 0.0 0.8
F02 A:J181101 2.2 0.8 0.8
F01 A:J181101 2.2 0.1 0.8
C08 A:J181101 2.2 86.2 0.8
O02 A:J181101 2.9 77.7 0.8
CG2 A:VAL360 3.0 36.8 1.0
C07 A:J181101 3.0 77.2 0.8
C10 A:J181101 3.3 75.6 0.8
S01 A:J181101 3.4 81.8 0.8
CB A:VAL360 3.4 38.4 1.0
H10 A:J181101 3.5 90.7 0.8
O03 A:J181101 4.0 83.3 0.8
CA D:ALA3 4.1 94.4 1.0
O D:HOH101 4.1 62.0 1.0
C13 A:J181101 4.2 68.3 0.8
N A:GLY361 4.3 45.0 1.0
C A:VAL360 4.3 45.6 1.0
CG1 A:VAL360 4.4 41.2 1.0
C11 A:J181101 4.5 69.6 0.8
C D:ALA3 4.5 92.7 1.0
CA A:VAL360 4.5 41.1 1.0
O D:ALA2 4.6 75.6 1.0
N D:ALA3 4.6 93.9 1.0
O A:VAL360 4.7 45.6 1.0
CA A:GLY361 4.8 43.7 1.0
O A:GLY361 4.8 53.1 1.0
N02 A:J181101 4.8 79.0 0.8
C A:GLY361 4.8 45.5 1.0
C D:ALA2 4.8 83.5 1.0
C12 A:J181101 4.9 67.5 0.8

Fluorine binding site 4 out of 6 in 6byz

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Fluorine binding site 4 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:0.3
occ:0.70
 F01 B:J181101 0.0 0.3 0.7
C09 B:J181101 1.3 0.3 0.7
F02 B:J181101 2.1 0.5 0.7
F03 B:J181101 2.2 0.4 0.7
C08 B:J181101 2.2 89.2 0.7
H10 B:J181101 2.6 95.9 0.7
C10 B:J181101 2.7 79.9 0.7
CA E:ALA3 2.9 0.3 1.0
C E:ALA3 3.1 96.2 1.0
C07 B:J181101 3.3 80.7 0.7
O E:ALA2 3.6 0.6 1.0
N E:ALA3 3.7 0.6 1.0
O02 B:J181101 3.9 71.9 0.7
C E:ALA2 3.9 0.8 1.0
CB B:VAL360 4.0 50.2 1.0
C11 B:J181101 4.0 77.3 0.7
CB E:ALA3 4.1 0.1 1.0
CG2 B:VAL360 4.1 47.9 1.0
O E:ALA3 4.2 90.7 1.0
S01 B:J181101 4.2 76.8 0.7
O B:GLY361 4.4 44.7 1.0
C13 B:J181101 4.5 75.5 0.7
N B:GLY361 4.5 50.6 1.0
CD1 B:ILE374 4.6 58.2 1.0
C B:GLY361 4.7 45.4 1.0
C12 B:J181101 4.7 75.2 0.7
H11 B:J181101 4.7 92.8 0.7
C B:VAL360 4.8 55.5 1.0
O03 B:J181101 4.9 80.2 0.7
CG1 B:VAL360 4.9 52.4 1.0
CA B:GLY361 5.0 46.3 1.0
CA B:VAL360 5.0 53.3 1.0

Fluorine binding site 5 out of 6 in 6byz

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Fluorine binding site 5 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:0.5
occ:0.70
 F02 B:J181101 0.0 0.5 0.7
C09 B:J181101 1.3 0.3 0.7
F01 B:J181101 2.1 0.3 0.7
F03 B:J181101 2.1 0.4 0.7
C08 B:J181101 2.2 89.2 0.7
H10 B:J181101 2.5 95.9 0.7
C10 B:J181101 2.7 79.9 0.7
CD1 B:ILE374 2.8 58.2 1.0
C B:GLY361 3.2 45.4 1.0
CA B:GLY361 3.4 46.3 1.0
O B:GLY361 3.4 44.7 1.0
C07 B:J181101 3.4 80.7 0.7
N B:GLY361 3.5 50.6 1.0
CA E:ALA3 3.5 0.3 1.0
N B:GLY362 3.5 50.4 1.0
C B:VAL360 3.9 55.5 1.0
C11 B:J181101 4.0 77.3 0.7
CG1 B:ILE374 4.1 57.2 1.0
N E:ALA3 4.1 0.6 1.0
CB E:ALA3 4.2 0.1 1.0
CA B:GLY362 4.2 53.1 1.0
O B:VAL360 4.3 58.8 1.0
CG2 B:VAL360 4.3 47.9 1.0
O B:ILE374 4.3 49.9 1.0
S01 B:J181101 4.3 76.8 0.7
CB B:VAL360 4.3 50.2 1.0
O B:GLY362 4.3 46.5 1.0
O03 B:J181101 4.4 80.2 0.7
C E:ALA3 4.4 96.2 1.0
C B:GLY362 4.4 49.2 1.0
O02 B:J181101 4.5 71.9 0.7
C13 B:J181101 4.5 75.5 0.7
H11 B:J181101 4.7 92.8 0.7
C E:ALA2 4.7 0.8 1.0
CA B:VAL360 4.7 53.3 1.0
C12 B:J181101 4.8 75.2 0.7
O E:ALA2 4.9 0.6 1.0

Fluorine binding site 6 out of 6 in 6byz

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Fluorine binding site 6 out of 6 in the Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Cysteine-Free Human Insulin-Degrading Enzyme in Complex with Substrate-Selective Macrocyclic Inhibitor 37 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1101

b:0.4
occ:0.70
 F03 B:J181101 0.0 0.4 0.7
C09 B:J181101 1.3 0.3 0.7
F02 B:J181101 2.1 0.5 0.7
F01 B:J181101 2.2 0.3 0.7
C08 B:J181101 2.2 89.2 0.7
O02 B:J181101 2.4 71.9 0.7
C07 B:J181101 2.7 80.7 0.7
S01 B:J181101 2.7 76.8 0.7
CG2 B:VAL360 2.8 47.9 1.0
O03 B:J181101 3.0 80.2 0.7
CB B:VAL360 3.4 50.2 1.0
CD1 B:ILE374 3.4 58.2 1.0
C10 B:J181101 3.5 79.9 0.7
H10 B:J181101 3.8 95.9 0.7
ND2 B:ASN376 3.8 1.0 1.0
C B:VAL360 4.0 55.5 1.0
C13 B:J181101 4.1 75.5 0.7
O B:VAL360 4.2 58.8 1.0
N B:GLY361 4.2 50.6 1.0
N02 B:J181101 4.3 70.5 0.7
CA B:VAL360 4.3 53.3 1.0
CG B:ASN376 4.5 97.9 1.0
CG1 B:VAL360 4.6 52.4 1.0
C11 B:J181101 4.6 77.3 0.7
CA B:GLY361 4.7 46.3 1.0
H08 B:J181101 4.7 79.5 0.7
H13 B:J181101 4.7 90.5 0.7
CG1 B:ILE374 4.8 57.2 1.0
C12 B:J181101 4.9 75.2 0.7
CB B:ASN376 4.9 78.2 1.0
CA E:ALA3 4.9 0.3 1.0
C06 B:J181101 5.0 66.1 0.7
C B:GLY361 5.0 45.4 1.0
H1A B:J181101 5.0 79.3 0.7

Reference:

J.P.Maianti, G.A.Tan, A.Vetere, A.J.Welsh, B.K.Wagner, M.A.Seeliger, D.R.Liu. Substrate-Selective Inhibitors That Reprogram the Activity of Insulin-Degrading Enzyme. Nat.Chem.Biol. V. 15 565 2019.
ISSN: ESSN 1552-4469
PubMed: 31086331
DOI: 10.1038/S41589-019-0271-0
Page generated: Sun Dec 13 12:46:12 2020

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