3M64

Human aldose reductase mutant T113V complexed with IDD393

• PDB DOI: https://doi.org/10.2210/pdb3M64/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-15 Released: 2011-03-09 
• Deposition Author(s): Koch, C., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.126 

Literature

Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase

Koch, C., Heine, A., Klebe, G.

(2011) Biochim Biophys Acta 1810: 879-887

• PubMed: 21684320 
• DOI: https://doi.org/10.1016/j.bbagen.2011.06.001
• Primary Citation of Related Structures:  
  3LEN, 3M0I, 3M64, 3MB9, 3MC5, 3P2V


• PubMed Abstract: 
  

  Flexibility is a common feature of proteins. For human aldose reductase, a variety of conformers have been observed in crystalline complexes with different inhibitors.

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Organizational Affiliation: 

Philipps-Universität, Department of Pharmaceutical Chemistry, Marburg, Germany.

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 kDa 
• Atom Count: 3,023 
• 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): 1  Gene Names: alr2 EC: 1.1.1.21
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
393	C [auth A]	(5-CHLORO-2-{[(3-NITROBENZYL)AMINO]CARBONYL}PHENOXY)ACETIC ACID C16 H13 Cl N2 O6 VABIMMIJVWNHFI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
393	BindingDB:  3M64	Kd: 14 (nM) from 1 assay(s)
		IC50: 6 (nM) from 1 assay(s)
		-TΔS: min: -1.25e+1, max: 36.89 (kJ/mol) from 3 assay(s)
		ΔH: -5.40e+1 (kJ/mol) from 1 assay(s)
		ΔG: min: -4.22e+1, max: -3.45e+1 (kJ/mol) from 4 assay(s)
	Binding MOAD:  3M64	Kd: 1510 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.174 
• R-Value Work: 0.126 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.37	α = 90
b = 66.36	β = 92.59
c = 47.2	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Koch, C., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-24
  Changes: Database references
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations