Crystal Structure of Human DPP4 Bound to TAK-294

Experimental Data Snapshot

  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 

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Identification of 3-aminomethyl-1,2-dihydro-4-phenyl-1-isoquinolones: a new class of potent, selective, and orally active non-peptide dipeptidyl peptidase IV inhibitors that form a unique interaction with Lys554.

Banno, Y.Miyamoto, Y.Sasaki, M.Oi, S.Asakawa, T.Kataoka, O.Takeuchi, K.Suzuki, N.Ikedo, K.Kosaka, T.Tsubotani, S.Tani, A.Funami, M.Tawada, M.Yamamoto, Y.Aertgeerts, K.Yano, J.Maezaki, H.

(2011) Bioorg Med Chem 19: 4953-4970

  • DOI: https://doi.org/10.1016/j.bmc.2011.06.059
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The design, synthesis, and structure-activity relationships of a new class of potent and orally active non-peptide dipeptidyl peptidase IV (DPP-4) inhibitors, 3-aminomethyl-1,2-dihydro-4-phenyl-1-isoquinolones, are described. We hypothesized that the 4-phenyl group of the isoquinolone occupies the S1 pocket of the enzyme, the 3-aminomethyl group forms an electrostatic interaction with the S2 pocket, and the introduction of a hydrogen bond donor onto the 6- or 7-substituent provides interaction with the hydrophilic region of the enzyme. Based on this hypothesis, intensive research focused on developing new non-peptide DPP-4 inhibitors has been carried out. Among the compounds designed in this study, we identified 2-[(3-aminomethyl-2-(2-methylpropyl)-1-oxo-4-phenyl-1,2-dihydro-6-isoquinolinyl)oxy]acetamide (35a) as a potent, selective, and orally bioavailable DPP-4 inhibitor, which exhibited in vivo efficacy in diabetic model rats. Finally, X-ray crystallography of 35a in a complex with the enzyme validated our hypothesized binding mode and identified Lys554 as a new target-binding site available for DPP-4 inhibitors.

  • Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 17-85 Jusohonmachi 2-Chome Yodogawa-ku, Yodogawa-ku, Osaka 532-8686, Japan.

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
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LUI

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
S [auth C],
T [auth D]
C22 H25 N3 O3
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
C8 H15 N O6
Binding Affinity Annotations 
IDSourceBinding Affinity
LUI PDBBind:  3OPM IC50: 240 (nM) from 1 assay(s)
BindingDB:  3OPM IC50: min: 47, max: 6.10e+4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.72 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.771α = 90
b = 122.557β = 115
c = 144.737γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-19
    Type: Initial release
  • Version 1.1: 2017-11-08
    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