Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37647.61 
• Atom Count: 2692 
• Residue Count: 316 
• Unique protein chains: 1

2NVD

Human Aldose Reductase complexed with novel naphtho[1,2-d]isothiazole acetic acid derivative (2)

• DOI: 10.2210/pdb2NVD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2006-11-12 Released: 2007-04-24 
• Deposition Author(s): Steuber, H., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.200 
• R-Value Work: 0.130 

Literature

Evidence for a novel binding site conformer of aldose reductase in ligand-bound state

Steuber, H., Zentgraf, M., La Motta, C., Sartini, S., Heine, A., Klebe, G.

(2007) J.Mol.Biol. 369: 186-197

• PubMed: 17418233 
• DOI: 10.1016/j.jmb.2007.03.021
• Primary Citation of Related Structures:  
  2NVC


• PubMed Abstract: 
  

Human aldose reductase (ALR2) has evolved as a promising therapeutic target for the treatment of diabetic long-term complications. The binding site of this enzyme possesses two main subpockets: the catalytic anion-binding site and the hydrophobic specificity pocket. The latter can be observed in the open or closed state, depending on the bound ligand. Thus, it exhibits a pronounced capability for induced-fit adaptations, whereas the catalytic pocket exhibits rigid properties throughout all known crystal structures. Here, we determined two ALR2 crystal structures at 1.55 and 1.65 A resolution, each complexed with an inhibitor of the recently described naphtho[1,2-d]isothiazole acetic acid series. In contrast to the original design hypothesis based on the binding mode of tolrestat (1), both inhibitors leave the specificity pocket in the closed state. Unexpectedly, the more potent ligand (2) extends the catalytic pocket by opening a novel subpocket. Access to this novel subpocket is mainly attributed to the rotation of an indole moiety of Trp 20 by about 35 degrees . The newly formed subpocket provides accommodation of the naphthyl portion of the ligand. The second inhibitor, 3, differs from 2 only by an extended glycolic ester functionality added to one of its carboxylic groups. However, despite this slight structural modification, the binding mode of 3 differs dramatically from that of the first inhibitor, but provokes less pronounced induced-fit adaptations of the binding cavity. Thus, a novel binding site conformation has been identified in a region where previous complex structures suggested only low adaptability of the binding pocket. Furthermore, the two ligand complexes represent an impressive example of how the slight change of a chemically extended side-chain at a given ligand scaffold can result in a dramatically altered binding mode. In addition, our study emphasizes the importance of crystal structure analysis for the translation of affinity data into structure-activity relationships.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1 (ALDR1) EC: 1.1.1.21
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
ITB	A	2-(CARBOXYMETHYL)-1-OXO-1,2-DIHYDRONAPHTHO[1,2-D]ISOTHIAZOLE-4-CARBOXYLIC ACID 3,3-DIOXIDE 2-CARBOXYMETHYL-1,3,3-TRIOXO-1,2-DIHYDRONAPHTHO[1,2-D]ISOTHIAZOLE-4-CARBOXYLIC ACID C14 H9 N O7 S ZTJGXDGAXGWOGR-UHFFFAOYSA-N
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ITB	IC50: 140 nM (99) BINDINGDB
ITB	IC50: 550 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.200 
• R-Value Work: 0.130 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 49.390	α = 90.00
b = 66.640	β = 91.88
c = 47.140	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-12 
• Released Date: 2007-04-24 
• Deposition Author(s): Steuber, H., Heine, A., Klebe, G.

Revision History 

• Version 1.0: 2007-04-24
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance