4PUW

Human Aldose Reductase complexed with a ligand with an IDD structure (2-[5-fluoro-2-(prop-2-ynylcarbamoyl)phenoxy]acetic acid) at 1.12 A

• PDB DOI: https://doi.org/10.2210/pdb4PUW/pdb

• Classification: Oxidoreductase/Oxidoreductase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-03-14 Released: 2015-04-08 
• Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.157 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 

Starting Model: experimental

Literature

Aldose Reductase: How expensive is the opening of the specificity pocket? IDD ligands under investigation

Rechlin, C., Heine, A., Scheer, F., Toth, P., Diederich, W., Klebe, G.

To be published.

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: 37.09 kDa 
• Atom Count: 3,063 
• Modelled Residue Count: 316 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
2WQ	B [auth A]	[5-fluoro-2-(prop-2-yn-1-ylcarbamoyl)phenoxy]acetic acid C12 H10 F N O4 PZTOBGBKDQCKIG-UHFFFAOYSA-N
CIT	C [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2WQ	BindingDB:  4PUW	-TΔS: min: -2.26e+1, max: 7.99 (kJ/mol) from 3 assay(s)
		ΔH: -4.62e+1 (kJ/mol) from 1 assay(s)
		ΔG: min: -4.09e+1, max: -3.13e+1 (kJ/mol) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 0.157 
• R-Value Work: 0.137 
• R-Value Observed: 0.138 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.411	α = 90
b = 66.688	β = 92.02
c = 47.353	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description