4PNZ

Human dipeptidyl peptidase IV/CD26 in complex with the long-acting inhibitor Omarigliptin (MK-3102)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Omarigliptin (MK-3102): A Novel Long-Acting DPP-4 Inhibitor for Once-Weekly Treatment of Type 2 Diabetes.

Biftu, T.Sinha-Roy, R.Chen, P.Qian, X.Feng, D.Kuethe, J.T.Scapin, G.Gao, Y.D.Yan, Y.Krueger, D.Bak, A.Eiermann, G.He, J.Cox, J.Hicks, J.Lyons, K.He, H.Salituro, G.Tong, S.Patel, S.Doss, G.Petrov, A.Wu, J.Xu, S.S.Sewall, C.Zhang, X.Zhang, B.Thornberry, N.A.Weber, A.E.

(2014) J.Med.Chem. 57: 3205-3212

  • DOI: 10.1021/jm401992e

  • PubMed Abstract: 
  • In our effort to discover DPP-4 inhibitors with added benefits over currently commercially available DPP-4 inhibitors, MK-3102 (omarigliptin), was identified as a potent and selective dipeptidyl peptidase 4 (DPP-4) inhibitor with an excellent pharmac ...

    In our effort to discover DPP-4 inhibitors with added benefits over currently commercially available DPP-4 inhibitors, MK-3102 (omarigliptin), was identified as a potent and selective dipeptidyl peptidase 4 (DPP-4) inhibitor with an excellent pharmacokinetic profile amenable for once-weekly human dosing and selected as a clinical development candidate. This manuscript summarizes the mechanism of action, scientific rationale, medicinal chemistry, pharmacokinetic properties, and human efficacy data for omarigliptin, which is currently in phase 3 clinical development.


    Organizational Affiliation

    Department of Discovery Chemistry, ‡Department of Metabolic Disorders, §Department of Pharmacology, ∥Department of Drug Metabolism, ⊥Basic Pharmaceutical Sciences, and #Department of Safety Assessment and Animal Resources, Merck & Co., Inc. , Whitehouse Station, New Jersey 08889, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 1 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2VH
Query on 2VH

Download SDF File 
Download CCD File 
A, B
(2R,3S,5R)-5-[2-(methylsulfonyl)-2,6-dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]-2-(2,4,5-trifluorophenyl)tetrahydro-2H-pyran-3-amine
C17 H19 F3 N4 O3 S
MHALHPKVYBFTTL-TYFHEEPYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.940α = 90.00
b = 125.777β = 90.00
c = 137.085γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
HKL-2000data scaling
HKL-2000data reduction
StructureStudiodata collection
REFMACrefinement
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-22 
  • Released Date: 2014-04-09 
  • Deposition Author(s): Scapin, G., Yan, Y.

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2014-05-07
    Type: Database references