2QKY

complex structure of dipeptidyl peptidase IV and a oxadiazolyl ketone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Synthesis, SAR, and X-ray structure of novel potent DPPIV inhibitors: oxadiazolyl ketones.

Koo, K.D.Kim, M.J.Kim, S.Kim, K.H.Hong, S.Y.Hur, G.C.Yim, H.J.Kim, G.T.Han, H.O.Kwon, O.H.Kwon, T.S.Koh, J.S.Lee, C.S.

(2007) Bioorg.Med.Chem.Lett. 17: 4167-4172

  • DOI: 10.1016/j.bmcl.2007.05.046

  • PubMed Abstract: 
  • Synthesis of a novel series of DPPIV inhibitors with 1,2,4- and 1,3,4-oxadiazolyl ketone derivatives and its structure-activity relationships are discussed. Compound 18h showed good inhibitory activity against DPPIV and favorable pharmacokinetic prop ...

    Synthesis of a novel series of DPPIV inhibitors with 1,2,4- and 1,3,4-oxadiazolyl ketone derivatives and its structure-activity relationships are discussed. Compound 18h showed good inhibitory activity against DPPIV and favorable pharmacokinetic properties. In vivo pharmacodynamic efficacy and co-crystal structure of compound 18h with DPPIV is also described.


    Organizational Affiliation

    LG Life Sciences, Ltd/R&D Park, 104-1 Munji-dong, Yuseong-gu, Daejeon 305-380, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4 (EC 3.4.14.5) (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP) (Dipeptidyl peptidase 4 soluble form) (Dipeptidyl peptidase IV soluble form)
A, B, C, D
728Homo sapiensMutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13Z
Query on 13Z

Download SDF File 
Download CCD File 
A, B, C, D
2-[(2-{(2S,4S)-2-[(R)-(5-tert-butyl-1,3,4-oxadiazol-2-yl)(hydroxy)methyl]-4-fluoropyrrolidin-1-yl}-2-oxoethyl)amino]-2-methylpropan-1-ol
C17 H29 F N4 O4
PHTMASAWZAGGEK-GMXVVIOVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
13ZKd: 0.247 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 73.178α = 76.30
b = 106.115β = 78.62
c = 132.051γ = 80.11
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description