Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37056.07 
• Atom Count: 2601 
• Residue Count: 316 
• Unique protein chains: 1

1T40

Crystal structure of human aldose reductase complexed with NADP and IDD552 at ph 5

• DOI: 10.2210/pdb1T40/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21


• Deposited: 2004-04-28 Released: 2004-08-03 
• Deposition Author(s): Ruiz, F., Hazemann, I., Mitschler, A., Chevrier, B., Schneider, T., Joachimiak, A., Karplus, M., Podjarny, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 

Literature

The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48.

Ruiz, F., Hazemann, I., Mitschler, A., Joachimiak, A., Schneider, T., Karplus, M., Podjarny, A.

(2004) Acta Crystallogr.,Sect.D 60: 1347-1354

• PubMed: 15272156 
• DOI: 10.1107/S0907444904011370
• Primary Citation of Related Structures:  
  1T41


• PubMed Abstract: 
  

The X-ray crystal structure of human aldose reductase (ALR2) in complex with the inhibitor IDD552 was determined using crystals obtained from two crystallization conditions with different pH values (pH 5 and 8). In both structures the charged carboxylic head of the inhibitor binds to the active site, making hydrogen-bond interactions with His110 and Tyr48 and electrostatic interactions with NADP+. There is an important difference between the two structures: the observation of a double conformation of the carboxylic acid moiety of the inhibitor at pH 8, with one water molecule interacting with the main configuration. This is the first time that a water molecule has been observed deep inside the ALR2 active site. Furthermore, in the configuration with the lower occupancy factor the difference electron-density map shows a clear peak (2.5sigma) for the H atom in the hydrogen bond between the inhibitor's carboxylic acid and the Tyr48 side-chain O atom. The position of this peak implies that this H atom is shared between both O atoms, indicating possible direct proton transfer from this residue to the inhibitor. This fact agrees with the model of the catalytic mechanism, in which the proton is donated by the Tyr48 hydroxyl to the substrate. These observations are useful both in drug design and in understanding the ALR2 mechanism.

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Organizational Affiliation: 

UPR de Biologie Structurale, IGBMC, CNRS INSERM ULP, 1 Rue Laurent Fries, BP 163, 67404 Illkirch, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aldose reductase	A	316	Homo sapiens	Mutation(s): 0  Gene Names: AKR1B1 (ALDR1) EC: 1.1.1.21
Find proteins for P15121 (Homo sapiens) Go to Gene View: AKR1B1 Go to UniProtKB:  P15121

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ID5	A	[5-FLUORO-2-({[(4,5,7-TRIFLUORO-1,3-BENZOTHIAZOL-2-YL)METHYL]AMINO}CARBONYL)PHENOXY]ACETIC ACID IDD552 C17 H10 F4 N2 O4 S ZCAGEXZTORJQDZ-UHFFFAOYSA-N
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ID5	IC50: 11 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.193 
• R-Value Work: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 50.000	α = 90.00
b = 67.240	β = 92.50
c = 47.780	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-28 
• Released Date: 2004-08-03 
• Deposition Author(s): Ruiz, F., Hazemann, I., Mitschler, A., Chevrier, B., Schneider, T., Joachimiak, A., Karplus, M., Podjarny, A.

Revision History 

• Version 1.0: 2004-08-03
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description