2ONC

Crystal structure of human DPP-4

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report



Literature

Discovery of alogliptin: a potent, selective, bioavailable, and efficacious inhibitor of dipeptidyl peptidase IV.

Feng, J., Zhang, Z., Wallace, M.B., Stafford, J.A., Kaldor, S.W., Kassel, D.B., Navre, M., Shi, L., Skene, R.J., Asakawa, T., Takeuchi, K., Xu, R., Webb, D.R., Gwaltney, S.L.

(2007) J Med Chem 50: 2297-2300

  • DOI: 10.1021/jm070104l
  • Primary Citation of Related Structures:  
    2ONC

  • PubMed Abstract: 

    • Alogliptin is a potent, selective inhibitor of the serine protease dipeptidyl peptidase IV (DPP-4). Herein, we describe the structure-based design and optimization of alogliptin and related quinazolinone-based DPP-4 inhibitors. Following an oral dose, th ...

    Alogliptin is a potent, selective inhibitor of the serine protease dipeptidyl peptidase IV (DPP-4). Herein, we describe the structure-based design and optimization of alogliptin and related quinazolinone-based DPP-4 inhibitors. Following an oral dose, these noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and a lowering of blood glucose in animal models of diabetes. Alogliptin is currently undergoing phase III trials in patients with type 2 diabetes.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 A, B, C, D731Homo sapiensMutation(s): 0 
Gene Names: DPP4, ADCP2, CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
GTEx:  ENSG00000197635
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G, H, I
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SY1
Query on SY1
Download Ideal Coordinates CCD File 
A, B, C, D
2-({2-[(3R)-3-AMINOPIPERIDIN-1-YL]-4-OXOQUINAZOLIN-3(4H)-YL}METHYL)BENZONITRILE
C21 H21 N5 O
OYNURZXTLNNKAP-QGZVFWFLSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SY1IC50 :  13   nM  PDBBind
SY1IC50:  13   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.357α = 90
b = 123.702β = 114.89
c = 145.358γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary