7EZR

Indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of Novel Indole Derivatives as Fructose-1,6-bisphosphatase Inhibitors and X-ray Cocrystal Structures Analysis.

Wang, X.Zhao, R.Ji, W.Zhou, J.Liu, Q.Zhao, L.Shen, Z.Liu, S.Xu, B.

(2022) ACS Med Chem Lett 13: 118-127

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00613
  • Primary Citation of Related Structures:  
    7EZF, 7EZP, 7EZR

  • PubMed Abstract: 

    Liver fructose-1,6-bisphosphatase (FBPase) is a key enzyme in the gluconeogenesis, and its inhibitors are expected to be novel antidiabetic agents. Herein, a series of new indole and benzofuran analogues were designed and synthesized to evaluate the inhibitory activity against FBPase. As a result, the novel FBPase inhibitors bearing N -acylsulfonamide moiety on the 3-position of the indole-2-carboxylic acid scaffold (compounds 22f and 22g ) were identified with IC 50 s at the submicromolar levels. Three X-ray crystal structures of the complexes were solved and revealed the structural basis for the inhibitory activity. The chemoinformatics analysis further disclosed the distinct binding features of this class of inhibitors, providing an insight for further modifications to create structurally distinct FBPase inhibitors with high potency and drug-like properties.


  • Organizational Affiliation

    Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fructose-1,6-bisphosphatase 1
A, B, C, D
338Homo sapiensMutation(s): 0 
Gene Names: FBP1FBP
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0H1 (Subject of Investigation/LOI)
Query on 0H1

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
5-ethyl-7-nitro-3-[3-oxidanylidene-3-(thiophen-2-ylsulfonylamino)propyl]-1H-indole-2-carboxylic acid
C18 H17 N3 O7 S2
WVTLJZSEUIFTKG-UHFFFAOYSA-N
FBP (Subject of Investigation/LOI)
Query on FBP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.27 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.902α = 90
b = 142.591β = 108.657
c = 73.575γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description