8XBK | pdb_00008xbk

Crystal Structure of Human Liver Fructose-1,6-bisphosphatase Complexed with a Covalent Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Guided Design of Affinity/Covalent-Bond Dual-Driven Inhibitors Targeting the AMP Site of FBPase.

Cao, H.Huang, Z.Liu, Z.Zhang, X.Ren, Y.Hameed, M.S.Rao, L.Makunga, N.P.Dobrikov, G.M.Wan, J.

(2024) J Med Chem 67: 20421-20437

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c01886
  • Primary Citation Related Structures: 
    8XBK

  • PubMed Abstract: 

    Fructose-1,6-bisphosphatase (FBPase) has attracted substantial interest as a target associated with cancer and type II diabetes. FBPase inhibitors targeting the AMP allosteric site have been documented, but their limited selectivity has raised concerns about adverse effects. To address this issue, we designed the affinity/covalent-bond dual-driven inhibitors based on the pharmacophore knowledge of the AMP pocket and neighboring cysteine residue (C179) of FBPase using the cysteine-targeting reactivity warhead screen followed by a structural optimization strategy. Pull-down and Western Blotting assays confirmed FBPase as a direct target in hepatic cells. X-ray cocrystallographic structure of FBPase- 11 and Cov_DOX calculation demonstrated that hydrogen bonding and π-π stacking were the predominant driving force for the inhibition of sulfonylurea-based FBPase covalent inhibitors, while covalent binding with C179 enhances the inhibitors' long-lasting hypoglycemic effects. Together, this work highlights the potential of affinity/covalent-bond dual-driven inhibitors in drug development and provides a promising approach for developing potent drugs targeting AMP-associated proteins.


  • Organizational Affiliation
    • State Key Laboratory of Green Pesticide, College of Chemistry, Central China Normal University, Wuhan 430079, China.

Macromolecule Content 

  • Total Structure Weight: 155.78 kDa 
  • Atom Count: 10,307 
  • Modeled Residue Count: 1,284 
  • 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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YR9
(Subject of Investigation/LOI)

Query on YR9



Download:Ideal Coordinates CCD File
E [auth A],
M [auth B],
V [auth C],
Y [auth D]
N-[2-[4-[(3-bromophenyl)carbamoylsulfamoyl]phenyl]ethyl]ethanamide
C17 H18 Br N3 O4 S
AXXRNELZCKOELA-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth D]
BA [auth D]
F [auth A]
G [auth A]
H [auth A]
AA [auth D],
BA [auth D],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
W [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
CA [auth D],
U [auth B],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.115α = 90
b = 82.95β = 90
c = 275.921γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
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
National Natural Science Foundation of China (NSFC)China21873035
National Natural Science Foundation of China (NSFC)China22377030

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Database references
  • Version 1.2: 2024-12-11
    Changes: Database references