2OGZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 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 accommod ...

    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.


    Organizational Affiliation

    Lilly Research Laboratories, A Division of Eli Lilly and Company, Indianapolis, IN 46285, USA. SHEEHAN_SCOTT@LILLY.COM



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase AB728Homo 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
U1N
Query on U1N

Download Ideal Coordinates CCD File 
A, B
4-[(3R)-3-{[2-(4-FLUOROPHENYL)-2-OXOETHYL]AMINO}BUTYL]BENZAMIDE
C19 H21 F N2 O2
OIWWNWQZJJKBTR-CYBMUJFWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
U1NIC50:  84   nM  Binding MOAD
U1NIC50 :  84   nM  PDBBind
U1NIC50:  84   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.595α = 90
b = 122.304β = 100.2
c = 112.721γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-01-09 
  • 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