3A29 | pdb_00003a29

Crystal structure of human liver FBPase in complex with tricyclic inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.247 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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Literature

Synthesis, SAR, and X-ray structure of tricyclic compounds as potent FBPase inhibitors

Tsukada, T., Takahashi, M., Takemoto, T., Kanno, O., Yamane, T., Kawamura, S., Nishi, T.

(2009) Bioorg Med Chem Lett 19: 5909-5912

  • DOI: https://doi.org/10.1016/j.bmcl.2009.08.081
  • Primary Citation Related Structures: 
    3A29

  • PubMed Abstract: 

    With the aim of discovering a novel class of fructose-1,6-bisphosphatase (FBPase) inhibitors, a series of compounds based on tricyclic scaffolds was synthesized. Extensive SAR studies led to the finding of 8l with an IC50 value of 0.013 microM against human FBPase. An X-ray crystallographic study revealed that 8l bound at AMP binding sites of human liver FBPase with hydrogen bonding interactions similar to AMP.

    • Organizational Affiliation: 
    • Medicinal Chemistry Research Laboratories I, Daiichi Sankyo Co., Ltd, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan.

Macromolecule Content 

  • Total Structure Weight: 148.11 kDa 
  • Atom Count: 10,148 
  • Modeled Residue Count: 1,273 
  • Deposited Residue Count: 1,348 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fructose-1,6-bisphosphatase 1
A, B, C, D
337Homo sapiensMutation(s): 0 
Gene Names: FBP1, FBP
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.247 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.289α = 90
b = 82.851β = 90
c = 277.253γ = 90
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description