Crystal structure of human dipeptidyl peptidase 4 (DPP IV) with potent alkynyl cyanopyrrolidine (ABT-279)

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of 2-[4-{{2-(2S,5R)-2-cyano-5-ethynyl-1-pyrrolidinyl]-2-oxoethyl]amino]- 4-methyl-1-piperidinyl]-4-pyridinecarboxylic acid (ABT-279): a very potent, selective, effective, and well-tolerated inhibitor of dipeptidyl peptidase-IV, useful for the treatment of diabetes.

Madar, D.J.Kopecka, H.Pireh, D.Yong, H.Pei, Z.Li, X.Wiedeman, P.E.Djuric, S.W.Von Geldern, T.W.Fickes, M.G.Bhagavatula, L.McDermott, T.Wittenberger, S.Richards, S.J.Longenecker, K.L.Stewart, K.D.Lubben, T.H.Ballaron, S.J.Stashko, M.A.Long, M.A.Wells, H.Zinker, B.A.Mika, A.K.Beno, D.W.Kempf-Grote, A.J.Polakowski, J.Segreti, J.Reinhart, G.A.Fryer, R.M.Sham, H.L.Trevillyan, J.M.

(2006) J Med Chem 49: 6416-6420

  • DOI: https://doi.org/10.1021/jm060777o
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Dipeptidyl peptidase-IV (DPP-IV) inhibitors are poised to be the next major drug class for the treatment of type 2 diabetes. Structure-activity studies of substitutions at the C5 position of the 2-cyanopyrrolidide warhead led to the discovery of potent inhibitors of DPP-IV that lack activity against DPP8 and DPP9. Further modification led to an extremely potent (Ki(DPP)(-)(IV) = 1.0 nM) and selective (Ki(DPP8) > 30 microM; Ki(DPP9) > 30 microM) clinical candidate, ABT-279, that is orally available, efficacious, and remarkably safe in preclinical safety studies.

  • Organizational Affiliation

    Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, Abbott Park, Illinois 60064-6001, USA. david.madar@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B, C, D
726Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on AXD

Download Ideal Coordinates CCD File 
C21 H29 N5 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
AXD PDBBind:  2I03 Ki: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.252α = 90
b = 126.994β = 96.56
c = 127.257γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description