1Z3N

Human aldose reductase in complex with NADP+ and the inhibitor lidorestat at 1.04 angstrom

• PDB DOI:  https://doi.org/10.2210/pdb1Z3N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-03-14 Released: 2006-03-14 
• Deposition Author(s): Van Zandt, M.C., Jones, M.L., Gunn, D.E., Geraci, L.S., Jones, J.H., Sawicki, D.R., Sredy, J., Jacot, J.L., Dicioccio, A.T., Petrova, T., Mitschler, A., Podjarny, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.125 
• R-Value Work: 0.091 
• R-Value Observed: 0.098 

Literature

Discovery of 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat) and congeners as highly potent and selective inhibitors of aldose reductase for treatment of chronic diabetic complications

Van Zandt, M.C., Jones, M.L., Gunn, D.E., Geraci, L.S., Jones, J.H., Sawicki, D.R., Sredy, J., Jacot, J.L., Dicioccio, A.T., Petrova, T., Mitschler, A., Podjarny, A.D.

(2005) J Med Chem 48: 3141-3152

• PubMed: 15857120 
• DOI: https://doi.org/10.1021/jm0492094
• Primary Citation of Related Structures:  
  1Z3N


• PubMed Abstract: 
  

Recent efforts to identify treatments for chronic diabetic complications have resulted in the discovery of a novel series of highly potent and selective 3-[(benzothiazol-2-yl)methyl]indole-N-alkanoic acid aldose reductase inhibitors. The lead candidate, 3-[(4,5,7-trifluorobenzothiazol-2-yl)methyl]indole-N-acetic acid (lidorestat, 9) inhibits aldose reductase with an IC(50) of 5 nM, while being 5400 times less active against aldehyde reductase, a related enzyme involved in the detoxification of reactive aldehydes. It lowers nerve and lens sorbitol levels with ED(50)'s of 1.9 and 4.5 mg/kg/d po, respectively, in the 5-day STZ-induced diabetic rat model. In a 3-month diabetic intervention model (1 month of diabetes followed by 2 months of drug treatment at 5 mg/kg/d po), it normalizes polyols and reduces the motor nerve conduction velocity deficit by 59% relative to diabetic controls. It has a favorable pharmacokinetic profile (F, 82%; t(1/2), 5.6 h; Vd, 0.694 L/kg) with good drug penetration in target tissues (C(max) in sciatic nerve and eye are 2.36 and 1.45 mug equiv/g, respectively, when dosed with [(14)C]lidorestat at 10 mg/kg po).

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Organizational Affiliation: 

The Institute for Diabetes Discovery, LLC, 23 Business Park Drive, Branford, Connecticut 06405, USA. michael.vanzandt@ ipd-discovery.com

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.3 kDa 
• Atom Count: 3,446 
• Modelled Residue Count: 316 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
aldose reductase	A	319	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
NDP	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
3NA	C [auth A]	{3-[(4,5,7-TRIFLUORO-1,3-BENZOTHIAZOL-2-YL)METHYL]-1H-INDOL-1-YL}ACETIC ACID C18 H11 F3 N2 O2 S KYHVTMFADJNSGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3NA	BindingDB:  1Z3N	IC50: min: 5, max: 2.70e+4 (nM) from 3 assay(s)
	Binding MOAD:  1Z3N	IC50: 5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.125 
• R-Value Work: 0.091 
• R-Value Observed: 0.098 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.14	α = 90
b = 67.34	β = 92.5
c = 47.88	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
SHELX	model building
SHELXL-97	refinement
X-PLOR	phasing
O	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Van Zandt, M.C., Jones, M.L., Gunn, D.E., Geraci, L.S., Jones, J.H., Sawicki, D.R., Sredy, J., Jacot, J.L., Dicioccio, A.T., Petrova, T., Mitschler, A., Podjarny, A.D.

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance