7WJV | pdb_00007wjv

Crystal structure of human liver FBPase complexed with an covalent inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

N -Acylamino Saccharin as an Emerging Cysteine-Directed Covalent Warhead and Its Application in the Identification of Novel FBPase Inhibitors toward Glucose Reduction.

Wen, W.Cao, H.Xu, Y.Ren, Y.Rao, L.Shao, X.Chen, H.Wu, L.Liu, J.Su, C.Peng, C.Huang, Y.Wan, J.

(2022) J Med Chem 65: 9126-9143

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00336
  • Primary Citation Related Structures: 
    7WJV

  • PubMed Abstract: 

    With a resurgence of covalent drugs, there is an urgent need for the identification of new moieties capable of cysteine bond formation. Herein, we report on the N -acylamino saccharin moieties capable of novel covalent reactions with cysteine. Their utility as alternative electrophilic warheads was demonstrated through the covalent modification of fructose-1,6-bisphosphatase (FBPase), a promising target associated with cancer and type 2 diabetes. The cocrystal structure of title compound W8 bound with FBPase unexpectedly revealed that the N -acylamino saccharin moiety worked as an electrophile warhead that covalently modified the noncatalytic C128 site in FBPase while releasing saccharin, suggesting a previously undiscovered covalent reaction mechanism of saccharin derivatives with cysteine. Treatment of title compound W8 displayed potent inhibition of glucose production in vitro and in vivo. This newly discovered reactive warhead supplements the current repertoire of cysteine covalent modifiers while avoiding some of the limitations generally associated with established moieties.


  • Organizational Affiliation
    • Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.

Macromolecule Content 

  • Total Structure Weight: 154.88 kDa 
  • Atom Count: 11,179 
  • Modeled Residue Count: 1,295 
  • Deposited Residue Count: 1,392 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructose-1,6-bisphosphatase 1
A, B, C, D
348Homo sapiensMutation(s): 0 
Gene Names: FBP1hCG_1640493
EC: 3.1.3.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09467 (Homo sapiens)
Explore P09467 
Go to UniProtKB:  P09467
PHAROS:  P09467
GTEx:  ENSG00000165140 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09467
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP

Query on AMP



Download:Ideal Coordinates CCD File
E [auth A],
I [auth B],
L [auth C],
N [auth D]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
LSA

Query on LSA



Download:Ideal Coordinates CCD File
F [auth A]1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE
C7 H5 N O3 S
CVHZOJJKTDOEJC-UHFFFAOYSA-N
PMQ
(Subject of Investigation/LOI)

Query on PMQ



Download:Ideal Coordinates CCD File
H [auth B]benzylcarbamic acid
C8 H9 N O2
RRIWSQXXBIFKQM-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth B],
M [auth C],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.641α = 90
b = 83.617β = 90
c = 278.717γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

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)China22177036

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-07-27
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary