3LEP

Human Aldose Reductase mutant T113C in complex with IDD388


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.109 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tracing the detail: how mutations affect binding modes and thermodynamic signatures of closely related aldose reductase inhibitors

Koch, C.Heine, A.Klebe, G.

(2011) J.Mol.Biol. 406: 700-712

  • DOI: 10.1016/j.jmb.2010.11.058
  • Primary Citation of Related Structures:  3LBO, 3LD5, 3LQG, 3LQL, 3LZ3, 3LZ5, 3M4H

  • PubMed Abstract: 
  • Improvements on the computational methods for affinity prediction from the structure of protein-ligand complexes require a better understanding of the nature of molecular interactions and biomolecular recognition principles. In the present contributi ...

    Improvements on the computational methods for affinity prediction from the structure of protein-ligand complexes require a better understanding of the nature of molecular interactions and biomolecular recognition principles. In the present contribution, the binding of two chemically closely related human aldose reductase inhibitors had been studied by high-resolution X-ray analysis (0.92-1.35 Ǻ) and isothermal titration calorimetry against a series of single-site mutants of the wild-type protein. A crucial threonine thought to be involved in a short bromine-to-oxygen halogen bond to the inhibitors in the wild type has been mutated to the structurally similar residues alanine, cysteine, serine and valine. Overall, structurally, the binding mode of the inhibitors is conserved; however, small but significant geometrical adaptations are observed as a consequence of the spatial and electronic changes at the mutation site. They involve the opening of a central bond angle and shifts in consequence of the lost or gained halogen bonds. Remarkably, the tiny structural changes are responded by partly strong modulation of the thermodynamic profiles. Even though the free energy of binding is maximally perturbed by only 7 kJ/mol, much stronger modulations and shifts in the enthalpy and entropy signatures are revealed, which indicate a pronounced enthalpy/entropy compensation. However, an explanatory correlation can be detected when facing these perturbances against the small structural changes. This also provides deeper insights into how single-site mutations can alter the selectivity profile of closely related ligands against a target protein.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Philipps-Universität, 35037 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aldose reductase
A
316Homo sapiensGene 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
388
Query on 388

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A
(2-{[(4-BROMO-2-FLUOROBENZYL)AMINO]CARBONYL}-5-CHLOROPHENOXY)ACETIC ACID
IDD388
C16 H12 Br Cl F N O4
ZLIGBZRXAQNUFO-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
BR
Query on BR

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Download CCD File 
A
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.109 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.270α = 90.00
b = 66.920β = 92.26
c = 47.340γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
MAR345dtbdata collection
SHELXL-97refinement
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-24
    Type: Database references