2OGZ | pdb_00002ogz

Crystal structure of DPP-IV complexed with Lilly aryl ketone inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2OGZ/pdb

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


• Deposited: 2007-01-09 Released: 2007-03-06 
• Deposition Author(s): Timm, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Discovery of non-covalent dipeptidyl peptidase IV inhibitors which induce a conformational change in the active site.

Sheehan, S.M., Mest, H.J., Watson, B.M., Klimkowski, V.J., Timm, D.E., Cauvin, A., Parsons, S.H., Shi, Q., Canada, E.J., Wiley, M.R., Ruehter, G., Evers, B., Petersen, S., Blaszczak, L.C., Pulley, S.R., Margolis, B.J., Wishart, G.N., Renson, B., Hankotius, D., Mohr, M., Zechel, J.C., Michael Kalbfleisch, J., Dingess-Hammond, E.A., Boelke, A., Weichert, A.G.

(2007) Bioorg Med Chem Lett 17: 1765-1768

• PubMed: 17239592 
• DOI: https://doi.org/10.1016/j.bmcl.2006.12.074
• Primary Citation of Related Structures:  
  2OGZ


• PubMed Abstract: 
  

  A series of non-covalent inhibitors of the serine protease dipeptidyl peptidase IV (DPP-IV) were found to adopt a U-shaped binding conformation in X-ray co-crystallization studies. Remarkably, Tyr547 undergoes a 70 degrees side-chain rotation to accommodate the inhibitor and allows access to a previously unexposed area of the protein backbone for hydrogen bonding.

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Organizational Affiliation: 

Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA. [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 (software)

Macromolecule Content

• Total Structure Weight: 169.58 kDa 
• Atom Count: 12,514 
• 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	A, B	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
U1N	C [auth A], D [auth B]	4-[(3R)-3-{[2-(4-FLUOROPHENYL)-2-OXOETHYL]AMINO}BUTYL]BENZAMIDE C19 H21 F N2 O2 OIWWNWQZJJKBTR-CYBMUJFWSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
U1N	BindingDB:  2OGZ	IC50: 84 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.268 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.595	α = 90
b = 122.304	β = 100.2
c = 112.721	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-06 
Deposition Author(s): Timm, D.E.

Revision History  

• Version 1.0: 2007-03-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary