3C43

Human dipeptidyl peptidase IV/CD26 in complex with a flouroolefin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV inhibitors

Edmondson, S.D.Wei, L.Xu, J.Shang, J.Xu, S.Pang, J.Chaudhary, A.Dean, D.C.He, H.Leiting, B.Lyons, K.A.Patel, R.A.Patel, S.B.Scapin, G.Wu, J.K.Beconi, M.G.Thornberry, N.A.Weber, A.E.

(2008) Bioorg.Med.Chem.Lett. 18: 2409-2413

  • DOI: 10.1016/j.bmcl.2008.02.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The synthesis, selectivity, rat pharmacokinetic profile, and drug metabolism profiles of a series of potent fluoroolefin-derived DPP-4 inhibitors (4) are reported. A radiolabeled fluoroolefin 33 was shown to possess a high propensity to form reactive ...

    The synthesis, selectivity, rat pharmacokinetic profile, and drug metabolism profiles of a series of potent fluoroolefin-derived DPP-4 inhibitors (4) are reported. A radiolabeled fluoroolefin 33 was shown to possess a high propensity to form reactive metabolites, thus revealing a potential liability for this class of DPP-4 inhibitors.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck & Co. Inc., PO Box 2000, Rahway, NJ 07065, USA. scott_edmondson@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 1 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download SDF File 
Download CCD File 
A
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
315
Query on 315

Download SDF File 
Download CCD File 
A, B
(2S,3S)-4-cyclopropyl-3-{(3R,5R)-3-[2-fluoro-4-(methylsulfonyl)phenyl]-1,2,4-oxadiazolidin-5-yl}-1-[(3S)-3-fluoropyrrolidin-1-yl]-1-oxobutan-2-amine
C20 H28 F2 N4 O4 S
PTAHVQJZNFGPHN-WFWWEWPISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
315IC50: 19 nM BINDINGMOAD
315IC50: 19 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.864α = 90.00
b = 125.835β = 90.00
c = 136.712γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXphasing
CNXrefinement
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance