3BCJ

Crystal structure of Aldose Reductase complexed with 2S4R (Stereoisomer of Fidarestat, 2S4S) at 0.78 A

• PDB DOI: https://doi.org/10.2210/pdb3BCJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-11-13 Released: 2008-04-08 
• Deposition Author(s): Zhao, H.T., El-Kabbani, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.78 Å
• R-Value Free: 0.110 
• R-Value Work: 0.100 
• R-Value Observed: 0.105 

Starting Model: experimental

Literature

Unusual Binding Mode of the 2S4R Stereoisomer of the Potent Aldose Reductase Cyclic Imide Inhibitor Fidarestat (2S4S) in the 15 K Crystal Structure of the Ternary Complex Refined at 0.78 A Resolution: Implications for the Inhibition Mechanism

Zhao, H.T., Hazemann, I., Mitschler, A., Carbone, V., Joachimiak, A., Ginell, S., Podjarny, A., El-Kabbani, O.

(2008) J Med Chem 51: 1478-1481

• PubMed: 18284183 
• DOI: https://doi.org/10.1021/jm701514k
• Primary Citation of Related Structures:  
  3BCJ


• PubMed Abstract: 
  

  The structure of human aldose reductase in complex with the 2 S4 R stereoisomer of the potent inhibitor Fidarestat ((2 S,4 S)-6-fluoro-2',5'-dioxospiro-[chroman-4,4'-imidazoline]-2-carboxamide) was determined at 15 K and a resolution of 0.78 A. The structure of the complex provides experimental evidence for the inhibition mechanism in which Fidarestat is initially bound neutral and then becomes negatively charged by donating the proton at the 1'-position nitrogen of the cyclic imide ring to the N2 atom of the catalytic His110.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Monash University,Vic 3052, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 37.11 kDa 
• Atom Count: 3,654 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  EC: 1.1.1.21 (PDB Primary Data), 1.1.1.372 (UniProt), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens) Explore P15121  Go to UniProtKB:  P15121
PHAROS:  P15121 GTEx:  ENSG00000085662

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FIS	D [auth A]	(2S,4R)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE C12 H10 F N3 O4 WAAPEIZFCHNLKK-QPUJVOFHSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FIS	BindingDB:  3BCJ	IC50: 1.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.78 Å
• R-Value Free: 0.110 
• R-Value Work: 0.100 
• R-Value Observed: 0.105 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.2	α = 90
b = 66.642	β = 91.67
c = 47.28	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Zhao, H.T., El-Kabbani, O.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description