4GQR

Human Pancreatic alpha-amylase in complex with myricetin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Order and disorder: differential structural impacts of myricetin and ethyl caffeate on human amylase, an antidiabetic target.

Williams, L.K.Li, C.Withers, S.G.Brayer, G.D.

(2012) J.Med.Chem. 55: 10177-10186

  • DOI: 10.1021/jm301273u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The increasing prevalence of diabetes has accelerated the search for new drugs derived from natural sources. To define the functional features of two such families of compounds, the flavonols and the ethyl caffeates, we have determined the high-resol ...

    The increasing prevalence of diabetes has accelerated the search for new drugs derived from natural sources. To define the functional features of two such families of compounds, the flavonols and the ethyl caffeates, we have determined the high-resolution structures of representative inhibitors in complex with human pancreatic α-amylase. Myricetin binds at the active site and interacts directly with the catalytic residues despite its bulky planar nature. Notably, it reduces the normal conformational flexibility of the adjacent substrate binding cleft. In contrast, bound ethyl caffeate acts by disordering precisely those polypeptide chain segments that make up the active site binding cleft. It also operates from binding sites far removed from the active site, a property not observed in any other class of human α-amylase inhibitor studied to date. Given the current inadequacy of drugs directed at diabetes, the use of optimized flavonols and ethyl caffeates may present an alternative therapeutic route.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pancreatic alpha-amylase
A
496Homo sapiensMutation(s): 0 
Gene 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
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MYC
Query on MYC

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A
3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE
2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE; 3,3',4',5,5',7-HEXAHYDROXYFLAVONE; MYRICETIN; CANNABISCETIN
C15 H10 O8
IKMDFBPHZNJCSN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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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 %)
MYCIC50: 30200 nM (96) BINDINGDB
MYCKi: 110000 nM BINDINGMOAD
MYCKi: 110000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.129α = 90.00
b = 67.373β = 90.00
c = 129.929γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
CNSrefinement
MOSFLMdata reduction
CNSphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references