3G0B

Crystal structure of dipeptidyl peptidase IV in complex with TAK-322


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV.

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

(2011) J Med Chem 54: 510-524

  • DOI: 10.1021/jm101016w
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The discovery of two classes of heterocyclic dipeptidyl peptidase IV (DPP-4) inhibitors, pyrimidinones and pyrimidinediones, is described. After a single oral dose, these potent, selective, and noncovalent inhibitors provide sustained reduction of pl ...

    The discovery of two classes of heterocyclic dipeptidyl peptidase IV (DPP-4) inhibitors, pyrimidinones and pyrimidinediones, is described. After a single oral dose, these potent, selective, and noncovalent inhibitors provide sustained reduction of plasma DPP-4 activity and lowering of blood glucose in animal models of diabetes. Compounds 13a, 27b, and 27j were selected for development.


    Organizational Affiliation

    Takeda San Diego, Inc., 10410 Science Center Drive, San Diego, California 92121, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B, C, D
740Homo sapiensMutation(s): 0 
Gene Names: ADCP2CD26DPP4
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS  P27487
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T22
Query on T22

Download CCD File 
A, B, C, D
2-({6-[(3R)-3-aminopiperidin-1-yl]-3-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl}methyl)benzonitrile
C18 H21 N5 O2
ZSBOMTDTBDDKMP-OAHLLOKOSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T22IC50:  3.4000000953674316   nM  BindingDB
T22IC50:  7   nM  PDBBind
T22IC50:  7   nM  BindingDB
T22IC50:  7.599999904632568   nM  BindingDB
T22IC50:  5.300000190734863   nM  BindingDB
T22IC50:  10   nM  BindingDB
T22IC50:  7   nM  Binding MOAD
T22IC50:  1   nM  BindingDB
T22IC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.686α = 90
b = 122.398β = 114.72
c = 144.01γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2016-04-06
    Changes: Non-polymer description