Complex of Aldose Reductase with NADP+ and simaltaneously bound competetive inhibitors Fidarestat and IDD594. Concentration of Fidarestat in soaking solution is less than concentration of IDD594.

Experimental Data Snapshot

  • Resolution: 0.85 Å
  • R-Value Free: 0.095 
  • R-Value Work: 0.082 
  • R-Value Observed: 0.082 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history


Crystal packing modifies ligand binding affinity: The case of aldose reductase.

Cousido-Siah, A.Petrova, T.Hazemann, I.Mitschler, A.Ruiz, F.X.Howard, E.Ginell, S.Atmanene, C.Van Dorsselaer, A.Sanglier-Cianferani, S.Joachimiak, A.Podjarny, A.

(2012) Proteins 80: 2552-2561

  • DOI: https://doi.org/10.1002/prot.24136
  • Primary Citation of Related Structures:  
    2PEV, 2PF8, 2PFH

  • PubMed Abstract: 

    The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.

  • Organizational Affiliation

    Department of Integrative Biology, IGBMC, CNRS, INSERM, Université de Strasbourg, Illkirch, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1
UniProt & NIH Common Fund Data Resources
Find proteins for P15121 (Homo sapiens)
Explore P15121 
Go to UniProtKB:  P15121
PHAROS:  P15121
GTEx:  ENSG00000085662 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
C21 H30 N7 O17 P3
Query on LDT

Download Ideal Coordinates CCD File 
D [auth A]IDD594
C16 H12 Br F2 N O3 S
Query on FID

Download Ideal Coordinates CCD File 
C12 H10 F N3 O4
Query on CIT

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
C6 H8 O7
Query on CL

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
FID BindingDB:  2PFH Kd: 16 (nM) from 1 assay(s)
IC50: min: 9, max: 35 (nM) from 5 assay(s)
-TΔS: min: -9.80e+0, max: 29.71 (kJ/mol) from 6 assay(s)
ΔH: min: -3.54e+1, max: -2.99e+1 (kJ/mol) from 2 assay(s)
ΔG: min: -4.67e+1, max: -2.93e+1 (kJ/mol) from 8 assay(s)
Binding MOAD:  2PFH Kd: 6.5 (nM) from 1 assay(s)
LDT Binding MOAD:  2PFH Kd: 61 (nM) from 1 assay(s)
BindingDB:  2PFH IC50: min: 3, max: 30 (nM) from 2 assay(s)
-TΔS: min: -2.26e+1, max: 7.99 (kJ/mol) from 3 assay(s)
ΔH: -4.62e+1 (kJ/mol) from 1 assay(s)
ΔG: min: -4.09e+1, max: -3.13e+1 (kJ/mol) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 0.85 Å
  • R-Value Free: 0.095 
  • R-Value Work: 0.082 
  • R-Value Observed: 0.082 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.147α = 90
b = 66.553β = 92.31
c = 47.238γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Database references
  • Version 1.4: 2012-10-17
    Changes: Database references
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description