4PNZ | pdb_00004pnz

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 (Depositor), 0.196 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4PNZ

Ligand Structure Quality Assessment 


This is version 2.2 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: https://doi.org/10.1021/jm401992e
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 173.7 kDa 
  • Atom Count: 13,862 
  • Modeled Residue Count: 1,455 
  • Deposited Residue Count: 1,456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 1 
Gene Names: ADCP2CD26DPP4
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
PHAROS:  P27487
GTEx:  ENSG00000197635 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Glycosylation
Glycosylation Sites: 7Go to GlyGen: P27487-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, E, F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2VH

Query on 2VH



Download:Ideal Coordinates CCD File
I [auth A],
M [auth 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
NAG

Query on NAG



Download:Ideal Coordinates CCD File
J [auth A]
K [auth A]
L [auth A]
N [auth B]
O [auth B]
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.197 (Depositor), 0.196 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary