4A5S

CRYSTAL STRUCTURE OF HUMAN DPP4 IN COMPLEX WITH A NOVAL HETEROCYCLIC DPP4 INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel Heterocyclic Dpp-4 Inhibitors for the Treatment of Type 2 Diabetes.

Sutton, J.M.Clark, D.E.Dunsdon, S.J.Fenton, G.Fillmore, A.Harris, N.V.Higgs, C.Hurley, C.A.Krintel, S.L.Mackenzie, R.E.Duttaroy, A.Gangl, E.Maniara, W.Sedrani, R.Namoto, K.Ostermann, N.Gerhartz, B.Sirockin, F.Trappe, J.Hassiepen, U.Baeschlin, D.K.

(2012) Bioorg.Med.Chem.Lett. 22: 1464

  • DOI: 10.1016/j.bmcl.2011.11.054

  • PubMed Abstract: 
  • Novel deazaxanthine-based DPP-4 inhibitors have been identified that are potent (IC(50) <10nM) and highly selective versus other dipeptidyl peptidases. Their synthesis and SAR are reported, along with initial efforts to improve the PK profile through ...

    Novel deazaxanthine-based DPP-4 inhibitors have been identified that are potent (IC(50) <10nM) and highly selective versus other dipeptidyl peptidases. Their synthesis and SAR are reported, along with initial efforts to improve the PK profile through decoration of the deazaxanthine core. Optimisation of compound 3a resulted in the identification of compound (S)-4i, which displayed an improved in vitro and ADME profile. Further enhancements to the PK profile were possible by changing from the deazahypoxanthine to the deazaxanthine template, culminating in compound 12g, which displayed good ex vivo DPP-4 inhibition and a superior PK profile in rat, suggestive of once daily dosing in man.


    Organizational Affiliation

    Argenta Discovery 2009 Ltd, Harlow CM19 5TR, UK. jon.sutton@glpg.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM
A, B
740Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N7F
Query on N7F

Download SDF File 
Download CCD File 
A, B
6-[(3S)-3-AMINOPIPERIDIN-1-YL]-5-BENZYL-4-OXO-3-(QUINOLIN-4-YLMETHYL)-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDINE-7-CARBONITRILE
C29 H27 N7 O
WRJSBPQWADEDBH-QFIPXVFZSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-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 %)
N7FIC50: 17 nM (99) BINDINGDB
N7FIC50: 17 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 97.183α = 90.00
b = 121.424β = 90.00
c = 190.699γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release