6UH4

B. theta Bile Salt Hydrolase with covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report

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This is version 1.3 of the entry. See complete history


Literature

Development of a covalent inhibitor of gut bacterial bile salt hydrolases.

Adhikari, A.A.Seegar, T.C.M.Ficarro, S.B.McCurry, M.D.Ramachandran, D.Yao, L.Chaudhari, S.N.Ndousse-Fetter, S.Banks, A.S.Marto, J.A.Blacklow, S.C.Devlin, A.S.

(2020) Nat Chem Biol 16: 318-326

  • DOI: https://doi.org/10.1038/s41589-020-0467-3
  • Primary Citation of Related Structures:  
    6UFY, 6UH4

  • PubMed Abstract: 

    Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria to study the effects of bile acids on host physiology. Here, we report the development of a covalent pan-inhibitor of gut bacterial BSHs. From a rationally designed candidate library, we identified a lead compound bearing an alpha-fluoromethyl ketone warhead that modifies BSH at the catalytic cysteine residue. This inhibitor abolished BSH activity in conventional mouse feces. Mice gavaged with a single dose of this compound displayed decreased BSH activity and decreased deconjugated bile acid levels in feces. Our studies demonstrate the potential of a covalent BSH inhibitor to modulate bile acid composition in vivo.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Choloylglycine hydrolase
A, B, C, D
336Bacteroides thetaiotaomicronMutation(s): 0 
Gene Names: cbh_1Btheta7330_00957SAMN02910322_01222
EC: 3.5.1.24
UniProt
Find proteins for A0A0P0ENF5 (Bacteroides thetaiotaomicron)
Explore A0A0P0ENF5 
Go to UniProtKB:  A0A0P0ENF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P0ENF5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QC7 (Subject of Investigation/LOI)
Query on QC7

Download Ideal Coordinates CCD File 
E [auth B](5R,6R)-6-[(1S,2R,4aS,4bS,7R,8aS,10R,10aS)-7,10-dihydroxy-1,2,4b-trimethyltetradecahydrophenanthren-2-yl]-5-methylheptan-2-one
C25 H44 O3
SZOBNGKCEOANMX-IBSCZREMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.51 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.58α = 90
b = 99.52β = 90
c = 162.12γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R35GM128618-02
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5R35CA220340-03

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-03-04
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description