8HAY

d4-bound btDPP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Work: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target.

Wang, K.Zhang, Z.Hang, J.Liu, J.Guo, F.Ding, Y.Li, M.Nie, Q.Lin, J.Zhuo, Y.Sun, L.Luo, X.Zhong, Q.Ye, C.Yun, C.Zhang, Y.Wang, J.Bao, R.Pang, Y.Wang, G.Gonzalez, F.J.Lei, X.Qiao, J.Jiang, C.

(2023) Science 381: eadd5787-eadd5787

  • DOI: https://doi.org/10.1126/science.add5787
  • Primary Citation of Related Structures:  
    7Y4F, 7Y4G, 8HAY

  • PubMed Abstract: 

    A mechanistic understanding of how microbial proteins affect the host could yield deeper insights into gut microbiota-host cross-talk. We developed an enzyme activity-screening platform to investigate how gut microbiota-derived enzymes might influence host physiology. We discovered that dipeptidyl peptidase 4 (DPP4) is expressed by specific bacterial taxa of the microbiota. Microbial DPP4 was able to decrease the active glucagon like peptide-1 (GLP-1) and disrupt glucose metabolism in mice with a leaky gut. Furthermore, the current drugs targeting human DPP4, including sitagliptin, had little effect on microbial DPP4. Using high-throughput screening, we identified daurisoline-d4 (Dau-d4) as a selective microbial DPP4 inhibitor that improves glucose tolerance in diabetic mice.


  • Organizational Affiliation

    Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Peking University, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
btDPP4
A, B, C, D
714Bacteroides thetaiotaomicronMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KYL (Subject of Investigation/LOI)
Query on KYL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C]
(1~{R})-1-[[4-[5-[[(1~{R})-6,7-dimethoxy-2-methyl-3,4-dihydro-1~{H}-isoquinolin-1-yl]methyl]-2-methoxy-phenoxy]phenyl]methyl]-6,7-dimethoxy-2-methyl-3,4-dihydro-1~{H}-isoquinoline
C39 H46 N2 O6
UHYCXSGUNAWVBW-CZNDPXEESA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.106α = 90
b = 149.411β = 103.74
c = 137.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82071658

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-30
    Changes: Data collection, Database references