5Y7J

Crystal structure of human DPP4 in complex with inhibitor2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.521 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Unique binding mode of Evogliptin with human dipeptidyl peptidase IV.

Lee, H.K.Kim, M.K.Kim, H.D.Kim, H.J.Kim, J.W.Lee, J.O.Kim, C.W.Kim, E.E.

(2017) Biochem.Biophys.Res.Commun. 494: 452-459

  • DOI: 10.1016/j.bbrc.2017.10.101
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Evogliptin ((R)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl) piperazine-2-one)) is a highly potent selective inhibitor of dipeptidyl peptidase IV (DPP4) that was approved for the treatment of type 2 diabetes in South Korea. ...

    Evogliptin ((R)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl) piperazine-2-one)) is a highly potent selective inhibitor of dipeptidyl peptidase IV (DPP4) that was approved for the treatment of type 2 diabetes in South Korea. In this study, we report the crystal structures of Evogliptin, DA-12166, and DA-12228 (S,R diastereomer of Evogliptin) complexed to human DPP4. Analysis of both the structures and inhibitory activities suggests that the binding of the trifluorophenyl moiety in the S 1 pocket and the piperazine-2-one moiety have hydrophobic interactions with Phe357 in the S 2 extensive subsite, and that the multiple hydrogen bonds made by the (R)-β-amine group in the S 2 pocket and the contacts made by the (R)-tert-butyl group with Arg125 contribute to the high potency observed for Evogliptin.


    Organizational Affiliation

    School of Life Sciences and Biotechnology Korea University, Seoul, Republic of Korea.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea; Dong-A Socio R&D Center, Yongin, Republic of Korea; School of Life Sciences and Biotechnology Korea University, Seoul, Republic of Korea.,Dong-A Socio R&D Center, Yongin, Republic of Korea.,Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea. Electronic address: eunice@kist.re.kr.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dipeptidyl peptidase 4
A, B, C, D
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8OL
Query on 8OL

Download SDF File 
Download CCD File 
A, B, C, D
(S)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl)piperazin-2-one
C19 H26 F3 N3 O3
LCDDAGSJHKEABN-WBMJQRKESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.521 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 123.238α = 90.00
b = 119.470β = 89.96
c = 131.773γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-08-17 
  • Released Date: 2019-03-20 
  • Deposition Author(s): Lee, H.K., Kim, E.E.

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references