2PF8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.095 
  • R-Value Work: 0.085 
  • R-Value Observed: 0.085 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 10.1002/prot.24136
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo sapiensMutation(s): 0 
Gene Names: AKR1B1ALDR1ALR2
EC: 1.1.1.21 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.372 (UniProt), 1.1.1.54 (UniProt)
Find proteins for P15121 (Homo sapiens)
Go to UniProtKB:  P15121
NIH Common Fund Data Resources
PHAROS  P15121
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
LDT
Query on LDT

Download CCD File 
A
IDD594
C16 H12 Br F2 N O3 S
JCZUIWYXULSXSW-UHFFFAOYSA-N
 Ligand Interaction
FID
Query on FID

Download CCD File 
A
(2S,4S)-2-AMINOFORMYL-6-FLUORO-SPIRO[CHROMAN-4,4'-IMIDAZOLIDINE]-2',5'-DIONE
C12 H10 F N3 O4
WAAPEIZFCHNLKK-UFBFGSQYSA-N
 Ligand Interaction
CIT
Query on CIT

Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LDTΔH:  46.20000076293945   kJ/mol  BindingDB
FIDIC50:  35   nM  BindingDB
FID-TΔS:  28.790000915527344   kJ/mol  BindingDB
LDTIC50:  30   nM  BindingDB
FIDΔG:  29.600000381469727   kJ/mol  BindingDB
FIDIC50:  35   nM  BindingDB
FID-TΔS:  5.659999847412109   kJ/mol  BindingDB
FID-TΔS:  29.709999084472656   kJ/mol  BindingDB
LDT-TΔS:  22.59000015258789   kJ/mol  BindingDB
LDTΔG:  40.900001525878906   kJ/mol  BindingDB
FIDΔG:  42.70000076293945   kJ/mol  BindingDB
LDTIC50:  3   nM  BindingDB
FIDΔG:  29.299999237060547   kJ/mol  BindingDB
FID-TΔS:  9.800000190734863   kJ/mol  BindingDB
FIDΔH:  35.400001525878906   kJ/mol  BindingDB
FIDKd:  6.5   nM  Binding MOAD
FIDKd:  16   nM  BindingDB
FIDIC50:  9   nM  BindingDB
FIDΔG:  38   kJ/mol  BindingDB
LDTKd:  61   nM  Binding MOAD
LDTΔG:  31.5   kJ/mol  BindingDB
LDT-TΔS:  7.989999771118164   kJ/mol  BindingDB
LDTΔG:  38.70000076293945   kJ/mol  BindingDB
FIDΔH:  29.899999618530273   kJ/mol  BindingDB
LDT-TΔS:  14.6899995803833   kJ/mol  BindingDB
FIDΔG:  38.900001525878906   kJ/mol  BindingDB
FIDΔG:  37.900001525878906   kJ/mol  BindingDB
FIDΔG:  46.70000076293945   kJ/mol  BindingDB
FIDΔG:  35.400001525878906   kJ/mol  BindingDB
FIDIC50:  30   nM  BindingDB
FID-TΔS:  19.399999618530273   kJ/mol  BindingDB
FID-TΔS:  0.6000000238418579   kJ/mol  BindingDB
LDTΔG:  31.299999237060547   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.85 Å
  • R-Value Free: 0.095 
  • R-Value Work: 0.085 
  • R-Value Observed: 0.085 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.339α = 90
b = 66.815β = 92.1
c = 47.378γ = 90
Software Package:
Software NamePurpose
AMoREphasing
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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: 2012-08-22
    Changes: Database references
  • Version 1.4: 2012-10-17
    Changes: Database references