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 
  • R-Value Observed: 0.110 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.jmb.2010.11.058
  • Primary Citation of Related Structures:  
    3LBO, 3LD5, 3LEP, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldose reductase316Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15121
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
B [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
388
Query on 388

Download Ideal Coordinates CCD File 
C [auth A](2-{[(4-BROMO-2-FLUOROBENZYL)AMINO]CARBONYL}-5-CHLOROPHENOXY)ACETIC ACID
C16 H12 Br Cl F N O4
ZLIGBZRXAQNUFO-UHFFFAOYSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
E [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
BR
Query on BR

Download Ideal Coordinates CCD File 
D [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
388 Binding MOAD:  3LEP Kd: 110 (nM) from 1 assay(s)
BindingDB:  3LEP IC50: min: 30, max: 400 (nM) from 2 assay(s)
-TΔS: min: -5.96e-1, max: 28.79 (kJ/mol) from 3 assay(s)
ΔH: -2.99e+1 (kJ/mol) from 1 assay(s)
ΔG: min: -4.67e+1, max: -2.93e+1 (kJ/mol) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.99 Å
  • R-Value Free: 0.130 
  • R-Value Work: 0.109 
  • R-Value Observed: 0.110 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.27α = 90
b = 66.92β = 92.26
c = 47.34γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-15
    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