Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73579.55 
• Atom Count: 5162 
• Residue Count: 630 
• Unique protein chains: 1

1EF3

FIDARESTAT BOUND TO HUMAN ALDOSE REDUCTASE

• DOI: 10.2210/pdb1EF3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus


• Deposited: 2000-02-06 Released: 2001-02-07 
• Deposition Author(s): Oka, M., Matsumoto, Y., Sugiyama, S., Tsuruta, N., Matsushima, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.278 
• R-Value Work: 0.186 

Literature

A potent aldose reductase inhibitor, (2S,4S)-6-fluoro-2', 5'-dioxospiro[chroman-4,4'-imidazolidine]-2-carboxamide (Fidarestat): its absolute configuration and interactions with the aldose reductase by X-ray crystallography.

Oka, M., Matsumoto, Y., Sugiyama, S., Tsuruta, N., Matsushima, M.

(2000) J.Med.Chem. 43: 2479-2483

• PubMed: 10882376 


• PubMed Abstract: 
  

The absolute configuration of the aldose reductase (AR) inhibitor, (+)-(2S,4S)-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxamide (fidarestat), was established indirectly by single-crystal X-ray analysis of (+)-(2S, 4S)-8-bromo-6-fluoro-2',5'-dioxospiro¿chroman-4, 4'-imidazolidine-2-carboxylic acid (1). The crystal structure of human AR complexed with fidarestat was determined, and the specific inhibition activity was discussed on the basis of the three-dimensional interactions between them. The structure clarified that fidarestat was located in the active site by hydrophilic and hydrophobic interactions and that the carbamoyl group of fidarestat was a very effective substituent for affinity to AR and for selectivity between AR and aldehyde reductase (AHR). Explanations for the differences between the observed activities of fidarestat and its stereoisomer 2 were suggested by computer modeling.

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Organizational Affiliation: 

Rational Drug Design Laboratories, 4-1-1, Misato, Matsukawa-machi, Fukushima 960-1242, Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ALDOSE REDUCTASE	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1 (ALDR1, ALR2) EC: 1.1.1.300, 1.1.1.372, 1.1.1.54
Find proteins for P15121 (Homo sapiens) Go to Gene View: AKR1B1 Go to UniProtKB:  P15121

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAP	A, B	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
FID	A, B	(2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE FIDARESTAT C12 H10 F N3 O4 WAAPEIZFCHNLKK-UFBFGSQYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FID	IC50: 9 - 35 nM (100) BINDINGDB
FID	Kd: 16 nM (100) BINDINGDB
FID	ΔG: -29.3 - -46.7 kJ/mol (100) BINDINGDB
FID	ΔH: -29.9 - -35.4 kJ/mol (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.278 
• R-Value Work: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 96.140	α = 90.00
b = 62.560	β = 101.60
c = 118.990	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-02-06 
• Released Date: 2001-02-07 
• Deposition Author(s): Oka, M., Matsumoto, Y., Sugiyama, S., Tsuruta, N., Matsushima, M.

Revision History 

• Version 1.0: 2001-02-07
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-01-31
  Type: Experimental preparation