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Sodium in PDB 5ism: Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor

Enzymatic activity of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor

All present enzymatic activity of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor:
3.4.14.5;

Protein crystallography data

The structure of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor, PDB code: 5ism was solved by G.Scapin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 118.274, 126.029, 137.273, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.1

Other elements in 5ism:

The structure of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor (pdb code 5ism). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor, PDB code: 5ism:

Sodium binding site 1 out of 1 in 5ism

Go back to Sodium Binding Sites List in 5ism
Sodium binding site 1 out of 1 in the Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human DPP4 in Complex with A Novel 5,5,6-Tricyclic Pyrrolidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na810

b:24.3
occ:1.00
O A:GLY490 2.4 20.2 1.0
O A:LEU491 2.5 19.4 1.0
C A:LEU491 3.2 19.0 1.0
C A:GLY490 3.5 18.9 1.0
CA A:LEU491 3.8 18.7 1.0
N A:ARG492 3.9 18.3 1.0
N A:LEU491 4.1 18.1 1.0
CA A:ARG492 4.2 18.1 1.0
CA A:GLY490 4.7 18.8 1.0
O A:HOH1332 4.8 40.2 1.0
O A:HOH1453 4.9 15.0 1.0

Reference:

J.M.Cox, H.D.Chu, J.T.Kuethe, Y.D.Gao, G.Scapin, G.Eiermann, H.He, X.Li, K.A.Lyons, J.Metzger, A.Petrov, J.K.Wu, S.Xu, R.Sinha-Roy, A.E.Weber, T.Biftu. The Discovery of Novel 5,6,5- and 5,5,6-Tricyclic Pyrrolidines As Potent and Selective Dpp-4 Inhibitors. Bioorg.Med.Chem.Lett. V. 26 2622 2016.
ISSN: ESSN 1464-3405
PubMed: 27106708
DOI: 10.1016/J.BMCL.2016.04.020
Page generated: Tue Dec 15 11:06:36 2020

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