2RIP

Structure of DPPIV in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report



Literature

Design and synthesis of potent amido- and benzyl-substituted cis-3-amino-4-(2-cyanopyrrolidide)pyrrolidinyl DPP-IV inhibitors.

Corbett, J.W.Dirico, K.Song, W.Boscoe, B.P.Doran, S.D.Boyer, D.Qiu, X.Ammirati, M.Vanvolkenburg, M.A.McPherson, R.K.Parker, J.C.Cox, E.D.

(2007) Bioorg Med Chem Lett 17: 6707-6713

  • DOI: 10.1016/j.bmcl.2007.10.063
  • Primary Citation of Related Structures:  
    2RIP

  • PubMed Abstract: 
  • The cis-3-amino-4-(2-cyanopyrrolidide)-pyrrolidine template has been shown to afford low nanomolar inhibitors of human DPP-IV that exhibit a robust PK/PD profile. An X-ray co-crystal structure of 5 confirmed the proposed mode of binding. The potent singl ...

    The cis-3-amino-4-(2-cyanopyrrolidide)-pyrrolidine template has been shown to afford low nanomolar inhibitors of human DPP-IV that exhibit a robust PK/PD profile. An X-ray co-crystal structure of 5 confirmed the proposed mode of binding. The potent single digit DPP-IV inhibitor 53 exhibited a preferred PK/PD profile in preclinical animal models and was selected for additional profiling.


    Organizational Affiliation

    Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 A729Homo sapiensMutation(s): 0 
Gene Names: DPPIVDPP4ADCP2CD26
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
4 N-Glycosylation Oligosaccharides Interaction
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
34Q
Query on 34Q

Download Ideal Coordinates CCD File 
A
(3R,4R)-4-(pyrrolidin-1-ylcarbonyl)-1-(quinoxalin-2-ylcarbonyl)pyrrolidin-3-amine
C18 H21 N5 O2
XDSKICAQKGYYJF-OLZOCXBDSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
34QIC50 :  65   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.22α = 90
b = 69.22β = 90
c = 409.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-10-12 
  • Released Date: 2008-03-18 
  • Deposition Author(s): Qiu, X.

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary