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Zinc in PDB 4dwk: Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester)

Enzymatic activity of Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester)

All present enzymatic activity of Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester):
3.4.24.56;

Protein crystallography data

The structure of Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester), PDB code: 4dwk was solved by Q.Guo, R.Deprez-Poulain, B.Deprez, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.45 / 3.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 261.511, 261.511, 91.721, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester) (pdb code 4dwk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester), PDB code: 4dwk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4dwk

Go back to Zinc Binding Sites List in 4dwk
Zinc binding site 1 out of 2 in the Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:2.0
occ:1.00
 OE2 A:GLU189 1.8 2.0 1.0
NE2 A:HIS112 1.8 24.3 1.0
OE1 A:GLU189 1.8 21.8 1.0
O A:HOH1234 1.9 14.4 1.0
NE2 A:HIS108 1.9 25.2 1.0
CD A:GLU189 2.2 14.9 1.0
CD2 A:HIS112 2.7 27.0 1.0
CD2 A:HIS108 2.8 28.8 1.0
CE1 A:HIS112 2.9 27.4 1.0
CE1 A:HIS108 3.1 25.9 1.0
OE1 A:GLN111 3.7 31.7 1.0
CG A:GLU189 3.9 18.7 1.0
CG A:HIS112 3.9 24.7 1.0
ND1 A:HIS112 3.9 24.3 1.0
CG A:HIS108 4.0 25.7 1.0
ND1 A:HIS108 4.1 24.2 1.0
NE2 A:GLN111 4.2 28.4 1.0
CD A:GLN111 4.3 29.6 1.0
OH A:TYR831 4.7 31.0 1.0
O A:HOH1211 4.7 18.1 1.0
CE1 A:TYR831 4.9 32.6 1.0
O A:HIS108 4.9 26.9 1.0
CB A:GLU189 4.9 24.9 1.0

Zinc binding site 2 out of 2 in 4dwk

Go back to Zinc Binding Sites List in 4dwk
Zinc binding site 2 out of 2 in the Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Cystein Free Insulin Degrading Enzyme with Compound BDM41671 ((S)-2-{2-[Carboxymethyl-(3-Phenyl-Propyl)-Amino]- Acetylamino}-3-(1H-Imidazol-4-Yl)-Propionic Acid Methyl Ester) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:2.0
occ:1.00
 OE1 B:GLU189 1.3 4.4 1.0
NE2 B:HIS108 1.9 23.9 1.0
O B:HOH1207 2.0 17.0 1.0
NE2 B:HIS112 2.1 30.1 1.0
CD B:GLU189 2.4 21.5 1.0
OE2 B:GLU189 2.8 21.6 1.0
CE1 B:HIS112 2.9 33.4 1.0
CD2 B:HIS108 2.9 29.3 1.0
CE1 B:HIS108 3.0 26.6 1.0
CD2 B:HIS112 3.1 32.6 1.0
CG B:GLU189 3.9 24.3 1.0
OE1 B:GLN111 3.9 31.2 1.0
ND1 B:HIS112 4.0 33.9 1.0
ND1 B:HIS108 4.1 27.6 1.0
CG B:HIS108 4.1 26.5 1.0
CG B:HIS112 4.1 32.3 1.0
NE2 B:GLN111 4.2 27.6 1.0
OH B:TYR831 4.2 49.5 1.0
CD B:GLN111 4.4 29.2 1.0
CE1 B:TYR831 4.7 45.3 1.0
CZ B:TYR831 4.9 46.5 1.0

Reference:

J.Charton, M.Gauriot, Q.Guo, N.Hennuyer, X.Marechal, J.Dumont, M.Hamdane, V.Pottiez, V.Landry, O.Sperandio, M.Flipo, L.Buee, B.Staels, F.Leroux, W.J.Tang, B.Deprez, R.Deprez-Poulain. Imidazole-Derived 2-[N-Carbamoylmethyl-Alkylamino]Acetic Acids, Substrate-Dependent Modulators of Insulin-Degrading Enzyme in Amyloid-Beta Hydrolysis. Eur.J.Med.Chem. V. 79 184 2014.
ISSN: ISSN 0223-5234
PubMed: 24735644
DOI: 10.1016/J.EJMECH.2014.04.009
Page generated: Wed Dec 16 05:14:49 2020

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