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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.04 kDa 
• Atom Count: 3242 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

4LAU

Crystal structure of human AR complexed with NADP+ and {2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid

• PDB DOI: 10.2210/pdb4LAU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-20 Released: 2014-04-30 
• Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Fanfrlik, J., Kolar, M., Hobza, P., Podjarny, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free: 0.142 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 

Literature

Modulation of aldose reductase inhibition by halogen bond tuning.

Fanfrlik, J., Kolar, M., Kamlar, M., Hurny, D., Ruiz, F.X., Cousido-Siah, A., Mitschler, A., Rezac, J., Munusamy, E., Lepsik, M., Matejicek, P., Vesely, J., Podjarny, A., Hobza, P.

(2013) ACS Chem Biol 8: 2484-2492

• PubMed: 23988122 
• DOI: 10.1021/cb400526n
• Primary Citation of Related Structures:  
  4LAU, 4LAZ, 4LB3, 4LB4, 4LBR, 4LBS


• PubMed Abstract: 
  

In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions. The role of the single halogen bond in AR-ligand binding was elucidated by advanced binding free energy calculations involving the semiempirical quantum chemical Hamiltonian. The results were complemented with ultrahigh-resolution X-ray crystallography and IC50 measurements. All of the AR inhibitors studied were shown by X-ray crystallography to bind in an identical manner. Further, it was demonstrated that it was possible to decrease the IC50 value by about 1 order of magnitude by tuning the strength of the halogen bond by a monoatomic substitution. The calculations revealed that the protein-ligand interaction energy increased upon the substitution of iodine for bromine or upon the addition of electron-withdrawing fluorine atoms to the ring. However, the effect on the binding affinity was found to be more complex due to the change of the solvation/desolvation properties within the ligand series. The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.

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Organizational Affiliation: 

Institute of Organic Chemistry and Biochemistry and Gilead Science Research Center, Academy of Sciences of the Czech Republic , Flemingovo nam. 2, 166 10 Prague 6, Czech Republic.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1, ALDR1, ALR2 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
W8X	C [auth A]	{2-[(4-bromobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid C16 H13 Br Cl N O4 PAOIFRPAIJVWIK-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
W8X	BindingDB:  4LAU	IC50: min: 550, max: 710 (nM) from 2 assay(s)
	Binding MOAD:  4LAU	IC50: 710 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.84 Å
• R-Value Free: 0.142 
• R-Value Work: 0.138 
• R-Value Observed: 0.138 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.328	α = 90
b = 67.047	β = 92.4
c = 47.347	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-20 
• Released Date: 2014-04-30 
Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Fanfrlik, J., Kolar, M., Hobza, P., Podjarny, A.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description