2OLE

Crystal Structure Of Human Dipeptidyl Peptidase IV (DPPIV) Complex With Cyclic Hydrazine Derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Synthesis, biological evaluation and structural determination of beta-aminoacyl-containing cyclic hydrazine derivatives as dipeptidyl peptidase IV (DPP-IV) inhibitors

Ahn, J.H.Shin, M.S.Jun, M.A.Jung, S.H.Kang, S.K.Kim, K.R.Rhee, S.D.Kang, N.S.Kim, S.Y.Sohn, S.K.Kim, S.G.Jin, M.S.Lee, J.O.Cheon, H.G.Kim, S.S.

(2007) Bioorg Med Chem Lett 17: 2622-2628

  • DOI: https://doi.org/10.1016/j.bmcl.2007.01.111
  • Primary Citation of Related Structures:  
    2OLE

  • PubMed Abstract: 

    Inhibitors of dipeptidyl peptidase IV (DPP-IV) have been shown to be effective treatments for type 2 diabetes. A series of beta-aminoacyl-containing cyclic hydrazine derivatives were synthesized and evaluated as DPP-IV inhibitors. One member of this series, (R)-3-amino-1-(2-benzoyl-1,2-diazepan-1-yl)-4-(2,4,5-trifluorophenyl)butan-1-one (10f), showed potent in vitro activity, good selectivity and in vivo efficacy in mouse models. Also, the binding mode of compound 10f was determined by X-ray crystallography.


  • Organizational Affiliation

    Bioorganic Science Division, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea. jhahn@krict.re.kr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 0 
Gene Names: chromosome 2
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
PHAROS:  P27487
GTEx:  ENSG00000197635 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KR2
Query on KR2

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2R)-4-(2-BENZOYL-1,2-DIAZEPAN-1-YL)-4-OXO-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-AMINE
C22 H24 F3 N3 O2
XXRHRPGYYNOBHO-QGZVFWFLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
KR2 PDBBind:  2OLE Ki: 56.2 (nM) from 1 assay(s)
BindingDB:  2OLE Ki: 56.2 (nM) from 1 assay(s)
IC50: 70 (nM) from 1 assay(s)
Binding MOAD:  2OLE Ki: 56.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.858α = 90
b = 126.545β = 99.64
c = 112.137γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations