3KC1

Crystal structure of human liver FBPase in complex with tricyclic inhibitor 19a

• PDB DOI: https://doi.org/10.2210/pdb3KC1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-20 Released: 2010-02-02 
• Deposition Author(s): Takahashi, M., Sone, J., Hanzawa, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 

Starting Model: experimental

Literature

Structure-based drug design of tricyclic 8H-indeno[1,2-d][1,3]thiazoles as potent FBPase inhibitors.

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

(2010) Bioorg Med Chem Lett 20: 1004-1007

• PubMed: 20045638 
• DOI: https://doi.org/10.1016/j.bmcl.2009.12.056
• Primary Citation of Related Structures:  
  3KBZ, 3KC0, 3KC1


• PubMed Abstract: 
  

  With the goal of improving metabolic stability and further enhancing FBPase inhibitory activity, a series of tricyclic 8H-indeno[1,2-d][1,3]thiazoles was designed and synthesized with the aid of structure-based drug design. Extensive SAR studies led to the discovery of 19a with an IC(50) value of 1nM against human FBPase. X-ray crystallographic studies revealed that high affinity of 19a was due to the hydrophobic interaction arising from better shape complementarity and to the hydrogen bonding network involving the side chain on the tricyclic scaffold.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.22 kDa 
• Atom Count: 10,173 
• Modelled Residue Count: 1,272 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A, B, C, D	337	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2T6	E [auth A], F [auth B], G [auth C], H [auth D]	{[(7-carbamoyl-8H-indeno[1,2-d][1,3]thiazol-4-yl)oxy]methyl}phosphonic acid C12 H11 N2 O5 P S APAVSBDDVLUPIF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2T6	PDBBind:  3KC1	IC50: 1 (nM) from 1 assay(s)
	BindingDB:  3KC1	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.262 
• R-Value Work: 0.228 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.358	α = 90
b = 83.213	β = 90
c = 278.147	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNX	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-02 
Deposition Author(s): Takahashi, M., Sone, J., Hanzawa, H.

Revision History  

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description