6YYD

Crystal structure of SAICAR Synthetase (PurC) from Mycobacterium abscessus in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Development of Inhibitors of SAICAR Synthetase (PurC) from Mycobacterium abscessus Using a Fragment-Based Approach.

Charoensutthivarakul, S.Thomas, S.E.Curran, A.Brown, K.P.Belardinelli, J.M.Whitehouse, A.J.Acebron-Garcia-de-Eulate, M.Sangan, J.Gramani, S.G.Jackson, M.Mendes, V.Floto, R.A.Blundell, T.L.Coyne, A.G.Abell, C.

(2022) ACS Infect Dis 8: 296-309

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00432
  • Primary Citation of Related Structures:  
    6YVQ, 6YX3, 6YY6, 6YY7, 6YY8, 6YY9, 6YYA, 6YYB, 6YYC, 6YYD, 6Z0Q, 6Z0R

  • PubMed Abstract: 

    Mycobacterium abscessus (Mab) has emerged as a challenging threat to individuals with cystic fibrosis. Infections caused by this pathogen are often impossible to treat due to the intrinsic antibiotic resistance leading to lung malfunction and eventually death. Therefore, there is an urgent need to develop new drugs against novel targets in Mab to overcome drug resistance and subsequent treatment failure. In this study, SAICAR synthetase (PurC) from Mab was identified as a promising target for novel antibiotics. An in-house fragment library screen and a high-throughput X-ray crystallographic screen of diverse fragment libraries were explored to provide crucial starting points for fragment elaboration. A series of compounds developed from fragment growing and merging strategies, guided by crystallographic information and careful hit-to-lead optimization, have achieved potent nanomolar binding affinity against the enzyme. Some compounds also show a promising inhibitory effect against Mab and Mtb. This work utilizes a fragment-based design and demonstrates for the first time the potential to develop inhibitors against PurC from Mab .


  • Organizational Affiliation

    Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoribosylaminoimidazole-succinocarboxamide synthase306Mycobacteroides abscessus ATCC 19977Mutation(s): 0 
Gene Names: purCMAB_0689
EC: 6.3.2.6
UniProt
Find proteins for B1MHW4 (Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CCUG 20993 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543 / L948))
Explore B1MHW4 
Go to UniProtKB:  B1MHW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1MHW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q0H (Subject of Investigation/LOI)
Query on Q0H

Download Ideal Coordinates CCD File 
B [auth A]4-azanyl-6-[1-[[3,4-bis(fluoranyl)phenyl]methyl]pyrazol-4-yl]pyrimidine-5-carbonitrile
C15 H10 F2 N6
XIBXZPKIDAMNCF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.708α = 90
b = 64.471β = 110.82
c = 48.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSwitzerlandFondation Botnar Grant No.6063
Other privateUnited KingdomCystic Fibrosis Trust SRC010

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Refinement description