2OLE

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

• PDB DOI: https://doi.org/10.2210/pdb2OLE/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2007-01-19 Released: 2008-01-22 
• Deposition Author(s): Kim, S.S., Ahn, J.H., Lee, J.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

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

• PubMed: 17331715 
• 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.

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Organizational Affiliation: 

Bioorganic Science Division, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 169.76 kDa 
• Atom Count: 12,510 
• Modelled Residue Count: 1,454 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	728	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KR2	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
ID	Source	Binding Affinity
KR2	BindingDB:  2OLE	Ki: 56.2 (nM) from 1 assay(s)
		IC50: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.858	α = 90
b = 126.545	β = 99.64
c = 112.137	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-22 
Deposition Author(s): Kim, S.S., Ahn, J.H., Lee, J.O.

Revision History  

• 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
• Version 1.3: 2024-11-06
  Changes: Structure summary