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Zinc in PDB 6thp: Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid

Enzymatic activity of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid

All present enzymatic activity of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid:
3.4.24.11;

Protein crystallography data

The structure of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid, PDB code: 6thp was solved by N.Schiering, C.Wiesmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.94 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.790, 109.390, 248.018, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.4

Other elements in 6thp:

The structure of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid (pdb code 6thp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid, PDB code: 6thp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6thp

Go back to Zinc Binding Sites List in 6thp
Zinc binding site 1 out of 2 in the Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn805

b:25.0
occ:1.00
 NE2 A:HIS587 1.9 30.2 1.0
OE1 A:GLU646 2.0 23.8 1.0
NE2 A:HIS583 2.0 23.7 1.0
O45 A:N9Q806 2.2 26.2 1.0
O46 A:N9Q806 2.6 23.4 1.0
C44 A:N9Q806 2.7 24.9 1.0
CD A:GLU646 2.7 24.4 1.0
CE1 A:HIS587 2.7 30.9 1.0
OE2 A:GLU646 2.8 23.8 1.0
CE1 A:HIS583 3.0 24.2 1.0
CD2 A:HIS587 3.1 30.2 1.0
CD2 A:HIS583 3.1 24.2 1.0
O A:HOH1008 3.9 39.1 1.0
ND1 A:HIS587 3.9 31.2 1.0
NE2 A:HIS711 4.0 23.3 1.0
ND1 A:HIS583 4.1 23.9 1.0
CG A:HIS587 4.1 31.3 1.0
C41 A:N9Q806 4.1 24.4 1.0
CG A:HIS583 4.2 26.2 1.0
CG A:GLU646 4.2 25.9 1.0
CD2 A:HIS711 4.3 24.0 1.0
C25 A:N9Q806 4.6 24.9 1.0
O A:HOH971 4.7 31.5 1.0
CA A:GLU646 4.7 27.0 1.0
CB A:ALA649 4.7 27.4 1.0
OE1 A:GLU584 4.7 28.1 1.0
CB A:GLU646 4.8 27.1 1.0
OE2 A:GLU584 4.8 29.6 1.0
O A:HOH1103 4.9 29.8 1.0

Zinc binding site 2 out of 2 in 6thp

Go back to Zinc Binding Sites List in 6thp
Zinc binding site 2 out of 2 in the Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Neprilysin in Complex with the Inhibitor (R)-4-(1-Carboxy-3-(3'- Chlorobiphenyl-4-Yl)Propan-2-Ylamino)-4-Oxobutanoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn805

b:31.8
occ:1.00
 O45 B:N9Q806 2.0 26.9 1.0
NE2 B:HIS587 2.0 37.3 1.0
OE1 B:GLU646 2.0 23.5 1.0
NE2 B:HIS583 2.1 27.0 1.0
O46 B:N9Q806 2.4 22.8 1.0
C44 B:N9Q806 2.5 25.2 1.0
CD B:GLU646 2.8 24.8 1.0
CE1 B:HIS587 2.8 36.7 1.0
OE2 B:GLU646 2.9 23.3 1.0
CD2 B:HIS583 3.0 26.2 1.0
CE1 B:HIS583 3.1 25.6 1.0
CD2 B:HIS587 3.2 35.3 1.0
C41 B:N9Q806 3.9 24.4 1.0
ND1 B:HIS587 4.0 36.4 1.0
NE2 B:HIS711 4.0 25.9 1.0
CG B:HIS583 4.1 27.7 1.0
ND1 B:HIS583 4.2 25.4 1.0
CG B:HIS587 4.2 35.1 1.0
CG B:GLU646 4.2 27.0 1.0
CD2 B:HIS711 4.2 25.8 1.0
O B:HOH969 4.4 30.4 1.0
C25 B:N9Q806 4.4 24.9 1.0
OE2 B:GLU584 4.6 33.3 1.0
CB B:ALA649 4.6 30.4 1.0
CA B:GLU646 4.7 29.9 1.0
CB B:GLU646 4.8 29.8 1.0
OE1 B:GLU584 4.9 33.3 1.0
O B:HOH1027 5.0 40.0 1.0

Reference:

N.Schiering, C.Wiesmann. Structure-Guided Design of Substituted Biphenyl Butanoic Acid Derivatives As Neprilysin Inhibitors Acs Med.Chem.Lett. 2020.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.9B00578
Page generated: Tue Oct 29 07:59:07 2024

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