2QKY

complex structure of dipeptidyl peptidase IV and a oxadiazolyl ketone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2QKY

  • 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 properti ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
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) ABCD728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
13Z
Query on 13Z

Download Ideal Coordinates 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 :  0.24699999392032623   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.178α = 76.3
b = 106.115β = 78.62
c = 132.051γ = 80.11
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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