6B1O

The structure of DPP4 in complex with Vildagliptin Analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A comparative study of the binding properties, dipeptidyl peptidase-4 (DPP-4) inhibitory activity and glucose-lowering efficacy of the DPP-4 inhibitors alogliptin, linagliptin, saxagliptin, sitagliptin and vildagliptin in mice.

Berger, J.P.SinhaRoy, R.Pocai, A.Kelly, T.M.Scapin, G.Gao, Y.D.Pryor, K.A.D.Wu, J.K.Eiermann, G.J.Xu, S.S.Zhang, X.Tatosian, D.A.Weber, A.E.Thornberry, N.A.Carr, R.D.

(2018) Endocrinol Diabetes Metab 1: e00002-e00002

  • DOI: 10.1002/edm2.2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Since 2006, DPP-4 inhibitors have become established therapy for the treatment of type 2 diabetes. Despite sharing a common mechanism of action, considerable chemical diversity exists amongst members of the DPP-4 inhibitor class, raising the question ...

    Since 2006, DPP-4 inhibitors have become established therapy for the treatment of type 2 diabetes. Despite sharing a common mechanism of action, considerable chemical diversity exists amongst members of the DPP-4 inhibitor class, raising the question as to whether structural differences may result in differentiated enzyme inhibition and antihyperglycaemic activity.


    Organizational Affiliation

    Present address: Janssen Pharmaceuticals, Inc. Titusville NJ USA.,Present address: Kallyope Inc. New York NY USA.,Merck& Co., Inc. Kenilworth NJ USA.,MSD A/S Copenhagen Denmark.,Present address: Takeda Pharmaceuticals International, Inc. Cambridge MA USA.,University College London UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8S
Query on C8S

Download SDF File 
Download CCD File 
A, B
(2S)-2-amino-1-[(1S,3S,5S)-3-(aminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(1r,3R,5S,7S)-3,5-dihydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-one
C18 H29 N3 O3
NFCLGRKAEZJOPE-KAARGAEXSA-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: 1.91 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 119.515α = 90.00
b = 123.342β = 90.00
c = 130.958γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-18 
  • Released Date: 2017-09-27 
  • Deposition Author(s): Scapin, G.

Revision History 

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references
  • Version 1.2: 2019-03-13
    Type: Data collection, Database references