6UQD | pdb_00006uqd

Co-complex of S. pyogenes 10782 streptopain bound with a SuFEx-based optimized small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.257 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.215 (Depositor) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6UQD

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Sulfur(VI) Fluoride Exchange (SuFEx)-Enabled High-Throughput Medicinal Chemistry.

Kitamura, S.Zheng, Q.Woehl, J.L.Solania, A.Chen, E.Dillon, N.Hull, M.V.Kotaniguchi, M.Cappiello, J.R.Kitamura, S.Nizet, V.Sharpless, K.B.Wolan, D.W.

(2020) J Am Chem Soc 142: 10899-10904

  • DOI: https://doi.org/10.1021/jacs.9b13652
  • Primary Citation Related Structures: 
    6UQD

  • PubMed Abstract: 

    Optimization of small-molecule probes or drugs is a synthetically lengthy, challenging, and resource-intensive process. Lack of automation and reliance on skilled medicinal chemists is cumbersome in both academic and industrial settings. Here, we demonstrate a high-throughput hit-to-lead process based on the biocompatible sulfur(VI) fluoride exchange (SuFEx) click chemistry. A high-throughput screening hit benzyl (cyanomethyl)carbamate ( K i = 8 μM) against a bacterial cysteine protease SpeB was modified with a SuFExable iminosulfur oxydifluoride [RN═S(O)F 2 ] motif, rapidly diversified into 460 analogs in overnight reactions, and the products were directly screened to yield drug-like inhibitors with 480-fold higher potency ( K i = 18 nM). We showed that the improved molecule is active in a bacteria-host coculture. Since this SuFEx linkage reaction succeeds on picomole scale for direct screening, we anticipate our methodology can accelerate the development of robust biological probes and drug candidates.


  • Organizational Affiliation
    • Laboratory of Advanced Food Process Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Nakaku, Sakai, Osaka 599-8570, Japan.

Macromolecule Content 

  • Total Structure Weight: 84.08 kDa 
  • Atom Count: 4,319 
  • Modeled Residue Count: 501 
  • Deposited Residue Count: 760 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Streptopain
A, B
380Streptococcus pyogenesMutation(s): 0 
Gene Names: speB
EC: 3.4.22.10
UniProt
Find proteins for P0C0J0 (Streptococcus pyogenes)
Explore P0C0J0 
Go to UniProtKB:  P0C0J0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C0J0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QF4
(Subject of Investigation/LOI)

Query on QF4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]
benzyl [(1S)-2-(3-{[(4-carbamoylpiperidin-1-yl)(fluoro)oxo-lambda~6~-sulfanylidene]amino}phenyl)-1-cyanoethyl]carbamate
C23 H26 F N5 O4 S
HBDGRYHWGNZLEM-TXRXYBTHSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.257 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.215 (Depositor) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.624α = 90
b = 115.516β = 112.58
c = 50.265γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-26
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description