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Zinc in PDB 4gs8: Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid

Enzymatic activity of Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid

All present enzymatic activity of Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid:
3.4.24.56;

Protein crystallography data

The structure of Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid, PDB code: 4gs8 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) 50.00 / 2.99
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 263.553, 263.553, 91.095, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 23.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid (pdb code 4gs8). 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 Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid, PDB code: 4gs8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4gs8

Go back to Zinc Binding Sites List in 4gs8
Zinc binding site 1 out of 2 in the Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:41.3
occ:1.00
 OE1 A:GLU189 1.8 23.8 1.0
NE2 A:HIS108 2.1 34.0 1.0
NE2 A:HIS112 2.1 32.3 1.0
O A:HOH1225 2.3 14.5 1.0
CD A:GLU189 2.5 29.8 1.0
OE2 A:GLU189 2.6 31.4 1.0
CD2 A:HIS108 3.1 35.2 1.0
CE1 A:HIS108 3.1 33.3 1.0
CD2 A:HIS112 3.1 31.4 1.0
CE1 A:HIS112 3.2 31.8 1.0
CG A:GLU189 4.0 31.1 1.0
ND1 A:HIS108 4.2 32.9 1.0
CG A:HIS108 4.2 32.4 1.0
O A:HOH1241 4.2 32.4 1.0
ND1 A:HIS112 4.3 32.2 1.0
CG A:HIS112 4.3 30.3 1.0
OE1 A:GLN111 4.3 34.6 1.0
OH A:TYR831 4.4 34.4 1.0
CE2 A:TYR831 4.5 34.3 1.0
NE2 A:GLN111 4.7 37.1 1.0
CB A:GLU189 4.8 32.6 1.0
CD A:GLN111 4.8 35.0 1.0
CZ A:TYR831 4.9 34.1 1.0

Zinc binding site 2 out of 2 in 4gs8

Go back to Zinc Binding Sites List in 4gs8
Zinc binding site 2 out of 2 in the Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure Analysis of Cysteine Free Insulin Degrading Enzyme (Ide) with Compound BDM43079 [{[(S)-2-(1H-Imidazol-4-Yl)-1-Methylcarbamoyl- Ethylcarbamoyl]-Methyl}-(3-Phenyl-Propyl)-Amino]-Acetic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:40.6
occ:1.00
 OE1 B:GLU189 1.7 44.2 1.0
NE2 B:HIS108 2.1 32.5 1.0
NE2 B:HIS112 2.1 38.9 1.0
O B:HOH1209 2.6 22.4 1.0
CD B:GLU189 2.7 43.8 1.0
CE1 B:HIS108 2.9 33.3 1.0
CD2 B:HIS112 3.0 37.4 1.0
CE1 B:HIS112 3.1 38.5 1.0
CD2 B:HIS108 3.2 32.4 1.0
OE2 B:GLU189 3.2 44.5 1.0
CG B:GLU189 4.1 40.1 1.0
ND1 B:HIS108 4.1 31.4 1.0
OH B:TYR831 4.2 42.9 1.0
CG B:HIS112 4.2 36.1 1.0
ND1 B:HIS112 4.2 37.1 1.0
CG B:HIS108 4.2 31.1 1.0
O B:HOH1232 4.3 42.7 1.0
CE2 B:TYR831 4.5 41.1 1.0
OE1 B:GLN111 4.5 35.1 1.0
NE2 B:GLN111 4.5 30.7 1.0
CZ B:TYR831 4.7 41.1 1.0
CB B:GLU189 4.8 37.5 1.0
CD B:GLN111 4.9 32.7 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 05:20:26 2020

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