3G5E | pdb_00003g5e

Human aldose reductase complexed with IDD 740 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3G5E/pdb

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


• Deposited: 2009-02-05 Released: 2009-03-24 
• Deposition Author(s): Podjarny, A.D., Van Zandt, M.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Discovery of [3-(4,5,7-trifluoro-benzothiazol-2-ylmethyl)-pyrrolo[2,3-b]pyridin-1-yl]acetic acids as highly potent and selective inhibitors of aldose reductase for treatment of chronic diabetic complications.

Van Zandt, M.C., Doan, B., Sawicki, D.R., Sredy, J., Podjarny, A.D.

(2009) Bioorg Med Chem Lett 19: 2006-2008

• PubMed: 19250825 
• DOI: https://doi.org/10.1016/j.bmcl.2009.02.037
• Primary Citation Related Structures: 
  3G5E


• PubMed Abstract: 
  

  Efforts to identify treatments for chronic diabetic complications have resulted in the discovery of a novel series of highly potent and selective [3-(4,5,7-trifluoro-benzothiazol-2-ylmethyl)-pyrrolo[2,3-b]pyridin-1-yl]acetic acid aldose reductase inhibitors. The lead candidate, [6-methyl-3-(4,5,7-trifluoro-benzothiazol-2-ylmethyl)-pyrrolo[2,3-b]pyridin-1-yl]acetic acid example 16, inhibits aldose reductase with an IC50 of 8 nM, while being inactive against aldehyde reductase (IC50>100 microM), a related enzyme involved in the detoxification of reactive aldehydes.

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Organizational Affiliation: 
• The Institute for Diabetes Discovery, LLC, 23 Business Park Drive, Branford, CT 06405, USA. [e-mail]

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: 37.3 kDa 
• Atom Count: 3,000 
• Modeled 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 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 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
Q74	C [auth A]	2-(3-((4,5,7-trifluorobenzo[d]thiazol-2-yl)methyl)-1H-pyrrolo[2,3-b]pyridin-1-yl)acetic acid C17 H10 F3 N3 O2 S IEVFQDJUDLCOQY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
Q74	BindingDB:  3G5E	IC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.144 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.016	α = 90
b = 67.204	β = 92.58
c = 47.861	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
X-PLOR	model building
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Podjarny, A.D., Van Zandt, M.C.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations