1U33

In situ extension as an approach for identifying novel alpha-amylase inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

In Situ Extension as an Approach for Identifying Novel alpha-Amylase Inhibitors.

Numao, S.Damager, I.Li, C.Wrodnigg, T.M.Begum, A.Overall, C.M.Brayer, G.D.Withers, S.G.

(2004) J.Biol.Chem. 279: 48282-48291

  • DOI: 10.1074/jbc.M406804200
  • Primary Citation of Related Structures:  1U2Y, 1U30

  • PubMed Abstract: 
  • A new approach for the discovery and subsequent structural elucidation of oligosaccharide-based inhibitors of alpha-amylases based upon autoglucosylation of known alpha-glucosidase inhibitors is presented. This concept, highly analogous to what is hy ...

    A new approach for the discovery and subsequent structural elucidation of oligosaccharide-based inhibitors of alpha-amylases based upon autoglucosylation of known alpha-glucosidase inhibitors is presented. This concept, highly analogous to what is hypothesized to occur with acarbose, is demonstrated with the known alpha-glucosidase inhibitor, d-gluconohydroximino-1,5-lactam. This was transformed from an inhibitor of human pancreatic alpha-amylase with a K(i) value of 18 mm to a trisaccharide analogue with a K(i) value of 25 mum. The three-dimensional structure of this complex was determined by x-ray crystallography and represents the first such structure determined with this class of inhibitors in any alpha-glycosidase. This approach to the discovery and structural analysis of amylase inhibitors should be generally applicable to other endoglucosidases and readily adaptable to a high throughput format.


    Organizational Affiliation

    Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-amylase, pancreatic
A
496Homo sapiensGene Names: AMY2A
EC: 3.2.1.1
Find proteins for P04746 (Homo sapiens)
Go to Gene View: AMY2A
Go to UniProtKB:  P04746
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LM2
Query on LM2

Download SDF File 
Download CCD File 
A
4'-O-METHYL-MALTOSYL-ALPHA (1,4)-(Z, 3S,4S,5R,6R)-3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-PIPERIDIN-2-ONE
4'-O-METHYL-MALTOSYL-ALPHA (1,4)-D-GLUCONHYDROXIMO-1,5-LACTAM
C19 H34 N2 O15
INFXBQXKGPGIEV-PXPLVWFRSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LM2Ki: 25000 nM BINDINGMOAD
LM2Ki: 25000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.200α = 90.00
b = 67.400β = 90.00
c = 130.200γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance