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 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report



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
  • Primary Citation of Related Structures:  
    4A5S

  • 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 dec ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIPEPTIDYL PEPTIDASE 4 SOLUBLE FORM AB740Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
NIH Common Fund Data Resources
PHAROS:  P27487
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
5 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N7F
Query on N7F

Download Ideal Coordinates 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
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
N7FIC50:  17   nM  Binding MOAD
N7FIC50:  17   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.183α = 90
b = 121.424β = 90
c = 190.699γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary