5Y7K

Crystal structure of human DPP4 in complex with inhibitor1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


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:  
    5Y7K, 5Y7H, 5Y7J

  • 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. In this study, we report the crystal structures of Evogliptin, DA-12166, and DA-12228 (S,R diastereomer of Evogliptin) complexed to human DPP4 ...

    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

    Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea. Electronic address: eunice@kist.re.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dipeptidyl peptidase 4A, B, C, D728Homo sapiensMutation(s): 0 
Gene Names: DPP4ADCP2CD26
EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens)
Explore P27487 
Go to UniProtKB:  P27487
PHAROS:  P27487
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8VU (Subject of Investigation/LOI)
Query on 8VU

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D](R)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl)piperazine-2-one
C19 H26 F3 N3 O3
LCDDAGSJHKEABN-MLGOLLRUSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
8VU BindingDB:  5Y7K IC50: 0.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.365α = 90
b = 131.92β = 89.99
c = 123.409γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data processing
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment  



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  (Full details and data files)

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