3NOX

Crystal structure of human DPP-IV in complex with Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.338 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of 6-(Aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidine-2-carboxamides as Potent, Selective Dipeptidyl Peptidase-4 (DPP4) Inhibitors.

Meng, W.Brigance, R.P.Chao, H.J.Fura, A.Harrity, T.Marcinkeviciene, J.O'Connor, S.P.Tamura, J.K.Xie, D.Zhang, Y.Klei, H.E.Kish, K.Weigelt, C.A.Turdi, H.Wang, A.Zahler, R.Kirby, M.S.Hamann, L.G.

(2010) J.Med.Chem. 53: 5620-5628

  • DOI: 10.1021/jm100634a

  • PubMed Abstract: 
  • Continued structure-activity relationship (SAR) exploration within our previously disclosed azolopyrimidine containing dipeptidyl peptidase-4 (DPP4) inhibitors led us to focus on an imidazolopyrimidine series in particular. Further study revealed tha ...

    Continued structure-activity relationship (SAR) exploration within our previously disclosed azolopyrimidine containing dipeptidyl peptidase-4 (DPP4) inhibitors led us to focus on an imidazolopyrimidine series in particular. Further study revealed that by replacing the aryl substitution on the imidazole ring with a more polar carboxylic ester or amide, these compounds displayed not only increased DPP4 binding activity but also significantly reduced human ether-a-go-go related gene (hERG) and sodium channel inhibitory activities. Additional incremental adjustment of polarity led to permeable molecules which exhibited favorable pharmacokinetic (PK) profiles in preclinical animal species. The active site binding mode of these compounds was determined by X-ray crystallography as exemplified by amide 24c. A subsequent lead molecule from this series, (+)-6-(aminomethyl)-5-(2,4-dichlorophenyl)-N-(1-ethyl-1H-pyrazol-5-yl)-7-methylimidazo[1,2-a]pyrimidine-2-carboxamide (24s), emerged as a potent, selective DPP4 inhibitor that displayed excellent PK profiles and in vivo efficacy in ob/ob mice.


    Organizational Affiliation

    Departments of Discovery Chemistry, Bristol-Myers Squibb, Research and Development, Princeton, New Jersey 08543-5400, USA. wei.meng@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2)
A, B
753Homo sapiensMutation(s): 0 
Gene Names: DPP4 (ADCP2, CD26)
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Go to Gene View: DPP4
Go to UniProtKB:  P27487
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6A5
Query on 6A5

Download SDF File 
Download CCD File 
A, B
Sa-(+)-(6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl)(morpholino)methanone
1-[5-(2,4-dichlorophenyl)-7-methyl-2-(morpholin-4-ylcarbonyl)imidazo[1,2-a]pyrimidin-6-yl]methanamine; 6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methyl-2-(morpholin-4-ylcarbonyl)imidazo[1,2-a]pyrimidin-4-ium-1-ide
C19 H19 Cl2 N5 O2
MNRQGIJBOGTUFQ-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6A5Ki: 2.2 nM (100) BINDINGDB
6A5Ki: 2.2 nM BINDINGMOAD
6A5Ki: 2.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.338 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.451α = 90.00
b = 67.072β = 90.00
c = 420.443γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-25 
  • Released Date: 2010-08-11 
  • Deposition Author(s): Klei, H.E.

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Other