4RPQ

Human Aldose Reductase complexed with a ligand with an IDD structure at 1.20 A (1)

• PDB DOI: https://doi.org/10.2210/pdb4RPQ/pdb

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


• Deposited: 2014-10-31 Released: 2015-11-18 
• Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 

Starting Model: experimental

Literature

Aldose Reductase: IDD ligands under investigation

Rechlin, C., Scheer, F., Heine, A., 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: 36.92 kDa 
• Atom Count: 2,866 
• Modelled Residue Count: 314 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldose reductase	A	315	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	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
3UH	B [auth A]	({3-[(3-nitrobenzyl)carbamoyl]biphenyl-4-yl}oxy)acetic acid C22 H18 N2 O6 YDJQSGAIAXGWHG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3UH	BindingDB:  4RPQ	Kd: 15 (nM) from 1 assay(s)
		-TΔS: -1.23e+1 (kJ/mol) from 1 assay(s)
		ΔH: -5.58e+1 (kJ/mol) from 1 assay(s)
		ΔG: -4.35e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.165 
• R-Value Work: 0.142 
• R-Value Observed: 0.143 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.554	α = 90
b = 66.796	β = 93.08
c = 47.191	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: 2015-11-18 
Deposition Author(s): Rechlin, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description