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: 36964.40 
• Atom Count: 2595 
• Residue Count: 316 
• Unique protein chains: 1

2PDJ

Human aldose reductase mutant L300A complexed with IDD393.

• DOI: 10.2210/pdb2PDJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2007-04-01 Released: 2008-04-01 
• Deposition Author(s): Steuber, H., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 

Literature

Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features.

Steuber, H., Heine, A., Podjarny, A., Klebe, G.

(2008) J.Mol.Biol. 379: 991-1016

• PubMed: 18495158 
• DOI: 10.1016/j.jmb.2008.03.063
• Primary Citation of Related Structures:  
  2PDY, 2PDX, 2PDW, 2PDU, 2PDQ, 2PDP, 2PDN, 2PDM, 2PDL, 2PDK, 2PDI, 2PDH, 2PDG, 2PDF, 2PDC, 2PDB, 2PD9, 2PD5


• PubMed Abstract: 
  

Inhibition of human aldose reductase (ALR2) evolved as a promising therapeutic concept to prevent late complications of diabetes. As well as appropriate affinity and bioavailability, putative inhibitors should possess a high level of selectivity for ALR2 over the related aldehyde reductase (ALR1). We investigated the selectivity-determining features by gradually mapping the residues deviating between the binding pockets of ALR1 and ALR2 into the ALR2 binding pocket. The resulting mutational constructs of ALR2 (eight point mutations and one double mutant) were probed for their influence towards ligand selectivity by X-ray structure analysis of the corresponding complexes and isothermal titration calorimetry (ITC). The binding properties of these mutants were evaluated using a ligand set of zopolrestat, a related uracil derivative, IDD388, IDD393, sorbinil, fidarestat and tolrestat. Our study revealed induced-fit adaptations within the mutated binding site as an essential prerequisite for ligand accommodation related to the selectivity discrimination of the ligands. However, our study also highlights the limits of the present understanding of protein-ligand interactions. Interestingly, binding site mutations not involved in any direct interaction to the ligands in various cases show significant effects towards their binding thermodynamics. Furthermore, our results suggest the binding site residues deviating between ALR1 and ALR2 influence ligand affinity in a complex interplay, presumably involving changes of dynamic properties and differences of the solvation/desolvation balance upon ligand binding.

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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): 1  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
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
393	A	(5-CHLORO-2-{[(3-NITROBENZYL)AMINO]CARBONYL}PHENOXY)ACETIC ACID IDD393 C16 H13 Cl N2 O6 VABIMMIJVWNHFI-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
393	IC50: 6 nM (99) BINDINGDB
393	Kd: 14 nM (99) BINDINGDB
393	ΔH: -54 kJ/mol (99) BINDINGDB
393	ΔG: -34.5 - -42.2 kJ/mol (99) BINDINGDB
393	Kd: 86.2 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 40.390	α = 76.11
b = 47.100	β = 76.68
c = 46.164	γ = 67.88

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-01 
• Released Date: 2008-04-01 
• Deposition Author(s): Steuber, H., Heine, A., Klebe, G.

Revision History 

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