5LIK

Crystal structure of human AKR1B10 complexed with NADP+ and the inhibitor MK181


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors.

Cousido-Siah, A.Ruiz, F.X.Fanfrlik, J.Gimenez-Dejoz, J.Mitschler, A.Kamlar, M.Vesely, J.Ajani, H.Pares, X.Farres, J.Hobza, P.Podjarny, A.D.

(2016) ACS Chem Biol 11: 2693-2705

  • DOI: 10.1021/acschembio.6b00382
  • Primary Citation of Related Structures:  
    5LIK, 5LIU, 5LIW, 5LIY, 5LIX

  • PubMed Abstract: 
  • Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhib ...

    Human enzyme aldo-keto reductase family member 1B10 (AKR1B10) has evolved as a tumor marker and promising antineoplastic target. It shares high structural similarity with the diabetes target enzyme aldose reductase (AR). Starting from the potent AR inhibitor IDD388, we have synthesized a series of derivatives bearing the same halophenoxyacetic acid moiety with an increasing number of bromine (Br) atoms on its aryl moiety. Next, by means of IC 50 measurements, X-ray crystallography, WaterMap analysis, and advanced binding free energy calculations with a quantum-mechanical (QM) approach, we have studied their structure-activity relationship (SAR) against both enzymes. The introduction of Br substituents decreases AR inhibition potency but improves it in the case of AKR1B10. Indeed, the Br atoms in ortho position may impede these drugs to fit into the AR prototypical specificity pocket. For AKR1B10, the smaller aryl moieties of MK181 and IDD388 can bind into the external loop A subpocket. Instead, the bulkier MK184, MK319, and MK204 open an inner specificity pocket in AKR1B10 characterized by a π-π stacking interaction of their aryl moieties and Trp112 side chain in the native conformation (not possible in AR). Among the three compounds, only MK204 can make a strong halogen bond with the protein (-4.4 kcal/mol, using QM calculations), while presenting the lowest desolvation cost among all the series, translated into the most selective and inhibitory potency AKR1B10 (IC 50 = 80 nM). Overall, SAR of these IDD388 polyhalogenated derivatives have unveiled several distinctive AKR1B10 features (shape, flexibility, hydration) that can be exploited to design novel types of AKR1B10 selective drugs.


    Organizational Affiliation

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS , 1 rue Laurent Fries 67404 CEDEX Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aldo-keto reductase family 1 member B10 X316Homo sapiensMutation(s): 2 
Gene Names: AKR1B10AKR1B11
EC: 1.1.1 (PDB Primary Data), 1.1.1.300 (UniProt), 1.1.1.54 (UniProt)
Find proteins for O60218 (Homo sapiens)
Explore O60218 
Go to UniProtKB:  O60218
NIH Common Fund Data Resources
PHAROS:  O60218
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
X
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
W8X
Query on W8X

Download Ideal Coordinates CCD File 
X
{2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid
C16 H13 Br Cl N O4
PAOIFRPAIJVWIK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
X
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
XL-PEPTIDE LINKINGC8 H18 N2 O2LYS
MLZ
Query on MLZ
XL-PEPTIDE LINKINGC7 H16 N2 O2LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
W8XIC50:  3700   nM  BindingDB
W8XIC50:  4500   nM  BindingDB
W8XIC50:  10200   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.661α = 90
b = 78.661β = 90
c = 48.221γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references