rat DPP-IV with xanthine mimetic inhibitor #7

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.253 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Xanthine mimetics as potent dipeptidyl peptidase IV inhibitors.

Kurukulasuriya, R.Rohde, J.J.Szczepankiewicz, B.G.Basha, F.Lai, C.Jae, H.S.Winn, M.Stewart, K.D.Longenecker, K.L.Lubben, T.W.Ballaron, S.J.Sham, H.L.von Geldern, T.W.

(2006) Bioorg Med Chem Lett 16: 6226-6230

  • DOI: https://doi.org/10.1016/j.bmcl.2006.09.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A series of xanthine mimetics containing 5,5 and 5,6 heterocycle fused imidazoles were synthesized as dipeptidyl peptidase IV inhibitors. Compound 7 is potent (h-DPPIV K(i)=2nM) and exhibits excellent selectivity and no species specificity against rat and human enzymes. The X-ray structure confirms that the binding mode of 7 to rat DPPIV is similar to the parent xanthines.

  • Organizational Affiliation

    Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6098, USA. ravi.kurukulasuriya@abbott.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
A, B
730Rattus norvegicusMutation(s): 0 
Find proteins for P14740 (Rattus norvegicus)
Explore P14740 
Go to UniProtKB:  P14740
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14740
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LIR

Download Ideal Coordinates CCD File 
C19 H21 N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
LIR PDBBind:  2I3Z Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.253 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.293α = 90
b = 207.293β = 90
c = 207.293γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

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
  • Version 1.4: 2018-01-24
    Changes: Structure summary