2HHA

The structure of DPP4 in complex with an oxadiazole inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of potent, selective, and orally bioavailable oxadiazole-based dipeptidyl peptidase IV inhibitors.

Xu, J.Wei, L.Mathvink, R.J.Edmondson, S.D.Eiermann, G.J.He, H.Leone, J.F.Leiting, B.Lyons, K.A.Marsilio, F.Patel, R.A.Patel, S.B.Petrov, A.Scapin, G.Wu, J.K.Thornberry, N.A.Weber, A.E.

(2006) Bioorg.Med.Chem.Lett. 16: 5373-5377

  • DOI: 10.1016/j.bmcl.2006.07.061

  • PubMed Abstract: 
  • A novel series of oxadiazole based amides have been shown to be potent DPP-4 inhibitors. The optimized compound 43 exhibited excellent selectivity over a variety of DPP-4 homologs.

    A novel series of oxadiazole based amides have been shown to be potent DPP-4 inhibitors. The optimized compound 43 exhibited excellent selectivity over a variety of DPP-4 homologs.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical protein DPP4
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
3TP
Query on 3TP

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Download CCD File 
A, B
(2S,3S)-3-{3-[4-(METHYLSULFONYL)PHENYL]-1,2,4-OXADIAZOL-5-YL}-1-OXO-1-PYRROLIDIN-1-YLBUTAN-2-AMINE
C17 H22 N4 O4 S
SQCDMTZMCHZYGO-FZMZJTMJSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3TPIC50: 122 nM (99) BINDINGDB
3TPIC50: 122 nM BINDINGMOAD
3TPIC50: 122 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 117.971α = 90.00
b = 125.584β = 90.00
c = 136.716γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
ADSCdata collection
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-06-28 
  • Released Date: 2006-09-19 
  • Deposition Author(s): Scapin, G.

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description