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Sodium in PDB 4pnz: Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

Enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)

All present enzymatic activity of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102):
3.4.14.5;

Protein crystallography data

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz was solved by G.Scapin, Y.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.15 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 117.940, 125.777, 137.085, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.7

Other elements in 4pnz:

The structure of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) (pdb code 4pnz). 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 Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102), PDB code: 4pnz:

Sodium binding site 1 out of 1 in 4pnz

Go back to Sodium Binding Sites List in 4pnz
Sodium binding site 1 out of 1 in the Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dipeptidyl Peptidase IV/CD26 in Complex with the Long-Acting Inhibitor Omarigliptin (Mk-3102) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:24.6
occ:1.00
 O A:GLY490 2.4 23.5 1.0
O A:LEU491 2.5 22.1 1.0
C A:LEU491 3.1 22.6 1.0
C A:GLY490 3.5 22.9 1.0
CA A:LEU491 3.8 17.8 1.0
N A:ARG492 3.9 19.1 1.0
N A:LEU491 4.1 18.2 1.0
CA A:ARG492 4.1 18.0 1.0
CA A:GLY490 4.7 18.2 1.0
O A:HOH957 4.9 19.1 1.0

Reference:

T.Biftu, R.Sinha-Roy, P.Chen, X.Qian, D.Feng, J.T.Kuethe, G.Scapin, Y.D.Gao, Y.Yan, D.Krueger, A.Bak, G.Eiermann, J.He, J.Cox, J.Hicks, K.Lyons, H.He, G.Salituro, S.Tong, S.Patel, G.Doss, A.Petrov, J.Wu, S.S.Xu, C.Sewall, X.Zhang, B.Zhang, N.A.Thornberry, A.E.Weber. Omarigliptin (Mk-3102): A Novel Long-Acting Dpp-4 Inhibitor For Once-Weekly Treatment of Type 2 Diabetes. J.Med.Chem. V. 57 3205 2014.
ISSN: ISSN 0022-2623
PubMed: 24660890
DOI: 10.1021/JM401992E
Page generated: Tue Dec 15 06:58:33 2020

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