2QJR | pdb_00002qjr

dipepdyl peptidase IV in complex with inhibitor PZF

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 3.1 of the entry. See complete history. 


Literature

(3R,4S)-4-(2,4,5-Trifluorophenyl)-pyrrolidin-3-ylamine inhibitors of dipeptidyl peptidase IV: synthesis, in vitro, in vivo, and X-ray crystallographic characterization.

Wright, S.W., Ammirati, M.J., Andrews, K.M., Brodeur, A.M., Danley, D.E., Doran, S.D., Lillquist, J.S., Liu, S., McClure, L.D., McPherson, R.K., Olson, T.V., Orena, S.J., Parker, J.C., Rocke, B.N., Soeller, W.C., Soglia, C.B., Treadway, J.L., Vanvolkenburg, M.A., Zhao, Z., Cox, E.D.

(2007) Bioorg Med Chem Lett 17: 5638-5642

  • DOI: https://doi.org/10.1016/j.bmcl.2007.07.081
  • Primary Citation of Related Structures:  
    2QJR

  • PubMed Abstract: 

    A series of pyrrolidine based inhibitors of dipeptidyl peptidase IV were developed from a high throughput screening hit for the treatment of type 2 diabetes. Potency, selectivity, and pharmacokinetic properties were optimized resulting in the identification of a pre-clinical candidate for further profiling.

    • Organizational Affiliation: 

    Pfizer Global Research and Development, Cardiovascular and Metabolic Diseases, MS 8220-3141, Eastern Point Road, Groton, CT 06340, USA.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 membrane form
A, B
748Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Glycosylation
Glycosylation Sites: 4
Go to GlyGen: P27487-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, E, F, G, H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-L-gulopyranuronic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
4N-Glycosylation
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
PZF BindingDB:  2QJR IC50: 37 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.47α = 90
b = 68.796β = 90
c = 422.611γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2008-07-29 
    • Deposition Author(s): Shenping, L.

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.2: 2014-12-17
    Changes: Non-polymer description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2022-04-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 3.1: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary