4QXI | pdb_00004qxi

Crystal structure of human AR complexed with NADP+ and AK198

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.87 Å
  • R-Value Free: 
    0.145 (Depositor), 0.148 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 
    0.134 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1021/acschembio.5b00151
  • Primary Citation 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.

    • 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.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP

Query on NAP


Download:Ideal Coordinates CCD File
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
I98

Query on I98


Download:Ideal Coordinates CCD File
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 
IDSourceBinding 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 (Depositor), 0.148 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.139 (DCC) 
  • R-Value Observed: 0.134 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.403α = 90
b = 66.542β = 92.34
c = 47.311γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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