Crystal structure of human dipeptidyl peptidase IV (DPPIV) complexed with cyanopyrrolidine (C5-pro-pro) inhibitor 21ag

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors.

Pei, Z.Li, X.Longenecker, K.Von Geldern, T.W.Wiedeman, P.E.Lubben, T.H.Zinker, B.A.Stewart, K.Ballaron, S.J.Stashko, M.A.Mika, A.K.Beno, D.W.Long, M.Wells, H.Kempf-Grote, A.J.Madar, D.J.McDermott, T.S.Bhagavatula, L.Fickes, M.G.Pireh, D.Solomon, L.R.Lake, M.R.Edalji, R.Fry, E.H.Sham, H.L.Trevillyan, J.M.

(2006) J Med Chem 49: 3520-3535

  • DOI: https://doi.org/10.1021/jm051283e
  • Primary Citation of Related Structures:  
    2G5P, 2G5T, 2G63

  • PubMed Abstract: 

    A series of (5-substituted pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidine (C5-Pro-Pro) analogues was discovered as dipeptidyl peptidase IV (DPPIV) inhibitors as a potential treatment of diabetes and obesity. X-ray crystallography data show that these inhibitors bind to the catalytic site of DPPIV with the cyano group forming a covalent bond with the serine residue of DPPIV. The C5-substituents make various interactions with the enzyme and affect potency, chemical stability, selectivity, and PK properties of the inhibitors. Optimized analogues are extremely potent with subnanomolar K(i)'s, are chemically stable, show very little potency decrease in the presence of plasma, and exhibit more than 1,000-fold selectivity against related peptidases. The best compounds also possess good PK and are efficacious in lowering blood glucose in an oral glucose tolerance test in ZDF rats.

  • Organizational Affiliation

    Department of Exploratory Pharmacokinetics and Pharmaceutics, Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-3500, USA. zhonghua.pei@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
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
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 ACF

Download Ideal Coordinates CCD File 
C18 H24 Cl N3 O4
Binding Affinity Annotations 
IDSourceBinding Affinity
ACF BindingDB:  2G5T Ki: 0.82 (nM) from 1 assay(s)
PDBBind:  2G5T Ki: 0.82 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.733α = 90
b = 126.788β = 99.49
c = 112.292γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    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