2I3Z

rat DPP-IV with xanthine mimetic inhibitor #7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.253 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 10.1016/j.bmcl.2006.09.024
  • Primary Citation of Related Structures:  
    2I3Z

  • 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 an ...

    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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) AB730Rattus norvegicusMutation(s): 0 
Gene Names: Dpp4Cd26
EC: 3.4.14.5
Find proteins for P14740 (Rattus norvegicus)
Explore P14740 
Go to UniProtKB:  P14740
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIR
Query on LIR

Download Ideal Coordinates CCD File 
A
2-[(3S)-3-AMINOPIPERIDIN-1-YL]-1-(2-CYANOBENZYL)-5-METHYL-4,6-DIOXO-3,4,5,6-TETRAHYDROPYRROLO[3,4-D]IMIDAZOL-1-IUM
C19 H21 N6 O2
WVRGIUWTFUXDGX-AWEZNQCLSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LIRKi :  2   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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