2QKY

complex structure of dipeptidyl peptidase IV and a oxadiazolyl ketone

• PDB DOI: https://doi.org/10.2210/pdb2QKY/pdb

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


• Deposited: 2007-07-12 Released: 2008-07-15 
• Deposition Author(s): Kim, K.-H., Hong, S.Y., Koo, K.D., Lee, C.-S., Kim, G.T., Han, H.O.

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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 

Starting Model: experimental

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

• PubMed: 17544668 
• DOI: https://doi.org/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 properties. In vivo pharmacodynamic efficacy and co-crystal structure of compound 18h with DPPIV is also described.

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Organizational Affiliation: 

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

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 (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 339.4 kDa 
• Atom Count: 24,275 
• Modelled Residue Count: 2,912 
• Deposited Residue Count: 2,912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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	728	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 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
13Z	E [auth A], F [auth B], G [auth C], H [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
13Z	PDBBind:  2QKY	Kd: 0.25 (nM) from 1 assay(s)
	BindingDB:  2QKY	IC50: 22 (nM) from 1 assay(s)

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 = 73.178	α = 76.3
b = 106.115	β = 78.62
c = 132.051	γ = 80.11

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Kim, K.-H., Hong, S.Y., Koo, K.D., Lee, C.-S., Kim, G.T., Han, H.O.

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
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary