5T4H

Human DPP4 in complex with ligand 34n


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Scaffold-hopping from xanthines to tricyclic guanines: A case study of dipeptidyl peptidase 4 (DPP4) inhibitors.

Pissarnitski, D.A.Zhao, Z.Cole, D.Wu, W.L.Domalski, M.Clader, J.W.Scapin, G.Voigt, J.Soriano, A.Kelly, T.Powles, M.A.Yao, Z.Burnett, D.A.

(2016) Bioorg.Med.Chem. 24: 5534-5545

  • DOI: 10.1016/j.bmc.2016.09.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Molecular modeling of unbound tricyclic guanine scaffolds indicated that they can serve as effective bioisosteric replacements of xanthines. This notion was further confirmed by a combination of X-ray crystallography and SAR studies, indicating that ...

    Molecular modeling of unbound tricyclic guanine scaffolds indicated that they can serve as effective bioisosteric replacements of xanthines. This notion was further confirmed by a combination of X-ray crystallography and SAR studies, indicating that tricyclic guanine DPP4 inhibitors mimic the binding mode of xanthine inhibitors, exemplified by linagliptin. Realization of the bioisosteric relationship between these scaffolds potentially will lead to a wider application of cyclic guanines as xanthine replacements in drug discovery programs for a variety of biological targets. Newly designed DPP4 inhibitors achieved sub-nanomolar potency range and demonstrated oral activity in vivo in mouse glucose tolerance test.


    Organizational Affiliation

    In Vitro Pharmacology, Merck Research Laboratories, 2000 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,In Vivo Pharmacology, Merck Research Laboratories, 2000 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,Department of Medicinal Chemistry, Merck Research Laboratories, 2000 Galloping Hill Rd., Kenilworth, NJ 07033, United States.,Department of Structural Chemistry, Merck Research Laboratories, 2000 Galloping Hill Rd., Kenilworth, NJ 07033, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B
728Homo 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
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
75J
Query on 75J

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Download CCD File 
A, B
2-({2-[(3R)-3-aminopiperidin-1-yl]-3-(but-2-yn-1-yl)-4-oxo-3,4-dihydro-5H-imidazo[2,1-b]purin-5-yl}methyl)benzonitrile
C24 H24 N8 O
FEXBDHCWKVFWPP-LJQANCHMSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 118.125α = 90.00
b = 126.008β = 90.00
c = 137.546γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-08-29 
  • Released Date: 2016-10-05 
  • Deposition Author(s): Scapin, G.

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references