Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.96 kDa 
• Atom Count: 2864 
• Modelled Residue Count: 315 
• Deposited Residue Count: 316 
• Unique protein chains: 1

2PDJ

Human aldose reductase mutant L300A complexed with IDD393.

• PDB DOI: 10.2210/pdb2PDJ/pdb

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


• 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 
• R-Value Observed: 0.177 

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:  
  2PD5, 2PD9, 2PDB, 2PDC, 2PDF, 2PDG, 2PDH, 2PDI, 2PDJ, 2PDK, 2PDL, 2PDM, 2PDN, 2PDP, 2PDQ, 2PDU, 2PDW, 2PDX, 2PDY


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 1  Gene Names: ALR2, AKR1B1, ALDR1 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	B [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
393	C [auth A]	(5-CHLORO-2-{[(3-NITROBENZYL)AMINO]CARBONYL}PHENOXY)ACETIC ACID C16 H13 Cl N2 O6 VABIMMIJVWNHFI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
393	Binding MOAD:  2PDJ	Kd: 86.2 (nM) from 1 assay(s)
	BindingDB:  2PDJ	Kd: 14 (nM) from 1 assay(s)
		IC50: 6 (nM) from 1 assay(s)
		-TΔS: min: -1.25e+1, max: 36.89 (kJ/mol) from 3 assay(s)
		ΔH: -5.40e+1 (kJ/mol) from 1 assay(s)
		ΔG: min: -4.22e+1, max: -3.45e+1 (kJ/mol) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.226 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.39	α = 76.11
b = 47.1	β = 76.68
c = 46.164	γ = 67.88

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
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
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations