2I3Z

rat DPP-IV with xanthine mimetic inhibitor #7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 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

  • 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 ra ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
A, B
730Rattus norvegicusMutation(s): 0 
Gene Names: Dpp4 (Cd26)
EC: 3.4.14.5
Find proteins for P14740 (Rattus norvegicus)
Go to UniProtKB:  P14740
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIR
Query on LIR

Download SDF File 
Download 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: 2.9 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.253 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 207.293α = 90.00
b = 207.293β = 90.00
c = 207.293γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Structure summary