2OQI | pdb_00002oqi

Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-constrained phenethylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.284 (Depositor), 0.276 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.230 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2OQI

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Discovery and Structure-Activity Relationships of Piperidinone- and Piperidine-Constrained Phenethylamines as Novel, Potent, and Selective Dipeptidyl Peptidase IV Inhibitors.

Pei, Z.Li, X.Geldern, T.W.Longenecker, K.Pireh, D.Stewart, K.D.Backes, B.J.Lai, C.Lubben, T.H.Ballaron, S.J.Beno, D.W.Kempf-Grote, A.J.Sham, H.L.Trevillyan, J.M.

(2007) J Med Chem 50: 1983-1987

  • DOI: https://doi.org/10.1021/jm061436d
  • Primary Citation Related Structures: 
    2OQI, 2OQV

  • PubMed Abstract: 

    Dipeptidyl peptidase IV (DPP4) inhibitors are emerging as a new class of therapeutic agents for the treatment of type 2 diabetes. They exert their beneficial effects by increasing the levels of active glucagon-like peptide-1 and glucose-dependent insulinotropic peptide, which are two important incretins for glucose homeostasis. Starting from a high-throughput screening hit, we were able to identify a series of piperidinone- and piperidine-constrained phenethylamines as novel DPP4 inhibitors. Optimized compounds are potent, selective, and have good pharmacokinetic profiles.


  • Organizational Affiliation
    • Metabolic Disease Research, Global Pharmaceutical Research and Development, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-3500, USA. zhonghua.pei@abbott.com

Macromolecule Content 

  • Total Structure Weight: 338.24 kDa 
  • Atom Count: 23,820 
  • Modeled Residue Count: 2,904 
  • Deposited Residue Count: 2,912 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
A, B, C, D
728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
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
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GGO

Query on GGO



Download:Ideal Coordinates CCD File
E [auth B](4R,5R)-5-AMINO-1-[2-(1,3-BENZODIOXOL-5-YL)ETHYL]-4-(2,4,5-TRIFLUOROPHENYL)PIPERIDIN-2-ONE
C20 H19 F3 N2 O3
DIRIFWIKLRTNMB-DYVFJYSZSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.284 (Depositor), 0.276 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.230 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.294α = 90
b = 127.3β = 96.45
c = 126.799γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.5: 2024-11-13
    Changes: Structure summary