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

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 

This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1021/jm101016w
  • Primary Citation of Related Structures:  
    3G0B, 3G0C, 3G0D, 3G0G

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B, C, D
740Homo sapiensMutation(s): 0 
Gene Names: ADCP2CD26DPP4
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
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H, I
E, F, G, H, I, J, K, L
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on T22

Download Ideal Coordinates CCD File 
AA [auth C],
GA [auth D],
Q [auth A],
V [auth B]
C18 H21 N5 O2
Query on NAG

Download Ideal Coordinates CCD File 
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
FA [auth D]
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
C8 H15 N O6
Binding Affinity Annotations 
IDSourceBinding Affinity
T22 BindingDB:  3G0B Kd: min: 2.4, max: 29 (nM) from 2 assay(s)
IC50: min: 1, max: 10 (nM) from 10 assay(s)
Binding MOAD:  3G0B IC50: 7 (nM) from 1 assay(s)
PDBBind:  3G0B IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary