High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.

Steuber, H.; Zentgraf, M.; Podjarny, A.; Heine, A.; Klebe, G.

doi:10.2210/pdb1z89/pdb

Macromolecule Content

Total Structure Weight: 36966.48
Atom Count: 2628
Residue Count: 316
Unique protein chains: 1

1Z89

Human Aldose Reductase complexed with novel Sulfonyl-pyridazinone Inhibitor

DOI: 10.2210/pdb1Z89/pdb

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

Deposited: 2005-03-30 Released: 2006-03-14
Deposition Author(s): Steuber, H., Zentgraf, M., Podjarny, A., Heine, A., Klebe, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.206
R-Value Work: 0.163

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.

Steuber, H., Zentgraf, M., Podjarny, A., Heine, A., Klebe, G.

(2006) J.Mol.Biol. 356: 45-56

PubMed: 16337231 Search on PubMed
DOI: 10.1016/j.jmb.2005.10.067
Primary Citation of Related Structures:
1Z8A

PubMed Abstract:

The crystal structure of a novel sulfonyl-pyridazinone inhibitor in complex with aldose reductase, the first enzyme of the polyol pathway, has been determined to 1.43 angstroms and 0.95 angstroms resolution. The ternary complex of inhibitor, cofactor and enzyme has been obtained by soaking of preformed crystals. Supposedly due to low solubility in the crystallisation buffer, in both structures the inhibitor shows reduced occupancy of 74% and 46% population, respectively. The pyridazinone head group of the inhibitor occupies the catalytic site, whereas the chloro-benzofuran moiety penetrates into the opened specificity pocket. The high-resolution structure provides some evidence that the pyridazinone group binds in a negatively charged deprotonated state, whereas the neighbouring His110 residue most likely adopts a neutral uncharged status. Since the latter structure is populated by the ligand to only 46%, a second conformation of the C-terminal ligand-binding region can be detected. This conformation corresponds to the closed state of the specificity pocket when no or only small ligands are bound to aldose reductase. The two conformational states are in good agreement with frames observed along a molecular dynamics trajectory describing the transition from closed to open situation. Accordingly, both geometries, superimposed in the averaged crystal structure, correspond to snapshots of the ligand-bound and the unbound state. Isothermal titration calorimetry has been applied to determine the binding constants of the investigated pyridazinone in comparison to the hydantoin sorbinil and the carboxylate-type inhibitors IDD 594 and tolrestat. The pyridazinone exhibits a binding affinity similar to those of tolrestat and sorbinil, and shows slightly reduced affinity compared to IDD 594. These studies elucidating the binding mode and providing information about protonation states of protein side-chains involved in binding of this novel class of inhibitors establish the platform for further structure-based drug design.

Organizational Affiliation:

Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany.

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
Protein Feature View Full Protein Feature View for P15121

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
NAP Query on NAP Download SDF File Download CCD File	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Ligand Interaction
62P Query on 62P Download SDF File Download CCD File	A	6-[(5-CHLORO-3-METHYL-1-BENZOFURAN-2-YL)SULFONYL]PYRIDAZIN-3(2H)-ONE C₁₃ H₉ Cl N₂ O₄ S FXFPQPNUMWQRAO-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
62P	ΔH: -54 kJ/mol (99) BINDINGDB
62P	ΔG: -34.5 - -42.2 kJ/mol (99) BINDINGDB
62P	IC50: 0.8 - 1 nM (99) BINDINGDB
62P	Ka: 1100000 M^-1 BINDINGMOAD

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.206
R-Value Work: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 49.400	α = 90.00
b = 66.900	β = 92.10
c = 47.400	γ = 90.00

Software Package:

Software Name	Purpose
CNS	phasing
SHELXL-97	refinement
SCALEPACK	data scaling
SHELX	model building
HKL-2000	data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

Deposited Date: 2005-03-30
Released Date: 2006-03-14
Deposition Author(s): Steuber, H., Zentgraf, M., Podjarny, A., Heine, A., Klebe, G.

Revision History

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-04-30
Type: Version format compliance
Version 1.2: 2011-07-13
Type: Version format compliance

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Deposit Data

Deposition Help & Resources

148969 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1Z89

Human Aldose Reductase complexed with novel Sulfonyl-pyridazinone Inhibitor

High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.

Entity ID: 1

Experimental Data

Structure Validation

Deposition Data

Revision History