4PNZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4PNZ

  • 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 pharmacokin ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 AB728Homo sapiensMutation(s): 1 
Gene Names: ADCP2CD26DPP4
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G
2 N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.94α = 90
b = 125.777β = 90
c = 137.085γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
REFMACrefinement
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary