Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 73.58 kDa 
• Atom Count: 5187 
• Modelled Residue Count: 630 
• Deposited Residue Count: 630 
• Unique protein chains: 1

1EF3

FIDARESTAT BOUND TO HUMAN ALDOSE REDUCTASE

• PDB DOI: 10.2210/pdb1EF3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.278 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 

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 
• DOI: 10.1021/jm990502r
• Primary Citation of Related Structures:  
  1EF3


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALDOSE REDUCTASE	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1, ALDR1, ALR2 EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (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

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
FID	BindingDB:  1EF3	Kd: 16 (nM) from 1 assay(s)
		IC50: min: 9, max: 35 (nM) from 5 assay(s)
		-TΔS: min: -9.80e+0, max: 29.71 (kJ/mol) from 6 assay(s)
		ΔH: min: -3.54e+1, max: -2.99e+1 (kJ/mol) from 2 assay(s)
		ΔG: min: -4.67e+1, max: -2.93e+1 (kJ/mol) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.278 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.14	α = 90
b = 62.56	β = 101.6
c = 118.99	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-31
  Changes: Experimental preparation