The structure of DPP4 in complex with Vildagliptin Analog

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 2.0 of the entry. See complete history


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: https://doi.org/10.1002/edm2.2
  • Primary Citation of Related Structures:  
    6B1E, 6B1O

  • 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 as to whether structural differences may result in differentiated enzyme inhibition and antihyperglycaemic activity.

  • Organizational Affiliation

    Present address: Janssen Pharmaceuticals, Inc. Titusville NJ USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4
A, B
728Homo sapiensMutation(s): 1 
Gene Names: DPP4ADCP2CD26
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
PHAROS:  P27487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27487
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
C, D, E, F, G
C, D, E, F, G, H, I, J, K
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8S (Subject of Investigation/LOI)
Query on C8S

Download Ideal Coordinates CCD File 
N [auth A],
P [auth B]
C18 H29 N3 O3
Query on NAG

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
O [auth B]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.515α = 90
b = 123.342β = 90
c = 130.958γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-03-13
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary