4QXI

Crystal structure of human AR complexed with NADP+ and AK198

• PDB DOI: https://doi.org/10.2210/pdb4QXI/pdb

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


• Deposited: 2014-07-21 Released: 2015-07-22 
• Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Fanfrlik, J., Hobza, P., Podjarny, A.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 0.145 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 

Starting Model: experimental

Literature

The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition.

Fanfrlik, J., Ruiz, F.X., Kadlcikova, A., Rezac, J., Cousido-Siah, A., Mitschler, A., Haldar, S., Lepsik, M., Kolar, M.H., Majer, P., Podjarny, A.D., Hobza, P.

(2015) ACS Chem Biol 10: 1637-1642

• PubMed: 25919404 
• DOI: https://doi.org/10.1021/acschembio.5b00151
• Primary Citation of Related Structures:  
  4QXI


• PubMed Abstract: 
  

  The effect of halogen-to-hydrogen bond substitution on the binding energetics and biological activity of a human aldose reductase inhibitor has been studied using X-ray crystallography, IC50 measurements, advanced binding free energy calculations, and simulations. The replacement of Br or I atoms by an amine (NH2) group has not induced changes in the original geometry of the complex, which made it possible to study the isolated features of selected noncovalent interactions in a biomolecular complex.

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Organizational Affiliation: 

†Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Science and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.99 kDa 
• Atom Count: 3,194 
• Modelled Residue Count: 314 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1, ALDR1 EC: 1.1.1.21 (PDB Primary Data), 1.1.1.372 (UniProt), 1.1.1.300 (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 GTEx:  ENSG00000085662

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
I98	C [auth A]	{2-[(4-amino-2-fluorobenzyl)carbamoyl]-5-chlorophenoxy}acetic acid C16 H14 Cl F N2 O4 GFJYPJDGRCZNDI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
I98	BindingDB:  4QXI	IC50: 1300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.87 Å
• R-Value Free: 0.145 
• R-Value Work: 0.134 
• R-Value Observed: 0.134 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.403	α = 90
b = 66.542	β = 92.34
c = 47.311	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-22 
Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Fanfrlik, J., Hobza, P., Podjarny, A.D.

Revision History  

• Version 1.0: 2015-07-22
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Refinement description