3OLG

Structures of human pancreatic alpha-amylase in complex with acarviostatin III03


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

Structures of human pancreatic alpha-amylase in complex with acarviostatins: Implications for drug design against type II diabetes.

Qin, X.Ren, L.Yang, X.Bai, F.Wang, L.Geng, P.Bai, G.Shen, Y.

(2011) J Struct Biol 174: 196-202

  • DOI: https://doi.org/10.1016/j.jsb.2010.11.020
  • Primary Citation of Related Structures:  
    3OLD, 3OLE, 3OLG, 3OLI

  • PubMed Abstract: 

    Human pancreatic α-amylase (HPA) catalyzes the hydrolysis of α-d-(1,4) glycosidic linkages in starch and is one of the major therapeutic targets for type II diabetes. Several acarviostatins isolated from Streptomyces coelicoflavus var. nankaiensis previously showed more potent inhibition of HPA than acarbose, which has been successfully used in clinical therapy. However, the molecular mechanisms by which acarviostatins inhibit HPA remains elusive. Here we determined crystal structures of HPA in complexes with a series of acarviostatin inhibitors (I03, II03, III03, and IV03). Structural analyses showed that acarviostatin I03 undergoes a series of hydrolysis and condensation reactions in the HPA active site, similar to acarbose, while acarviostatins II03, III03, and IV03 likely undergo only hydrolysis reactions. On the basis of structural analysis combined with kinetic assays, we demonstrate that the final modified product with seven sugar rings is best suited for occupying the full active site and shows the most efficient inhibition of HPA. Our high resolution structures reported here identify first time an interaction between an inhibitor and subsite-4 of the HPA active site, which we show makes a significant contribution to the inhibitory effect. Our results provide important information for the design of new drugs for the treatment of type II diabetes or obesity.


  • Organizational Affiliation

    Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University, Tianjin 300071, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pancreatic alpha-amylase496Homo sapiensMutation(s): 1 
Gene Names: AMY2A
EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04746 (Homo sapiens)
Explore P04746 
Go to UniProtKB:  P04746
PHAROS:  P04746
GTEx:  ENSG00000243480 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04746
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G96906VH
GlyCosmos:  G96906VH
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
C
3N/A
Glycosylation Resources
GlyTouCan:  G51132RN
GlyCosmos:  G51132RN
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
D
4N/A
Glycosylation Resources
GlyTouCan:  G69211UR
GlyCosmos:  G69211UR
GlyGen:  G69211UR
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose
E
3N/A
Glycosylation Resources
GlyTouCan:  G00395FS
GlyCosmos:  G00395FS
GlyGen:  G00395FS
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download Ideal Coordinates CCD File 
L [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
HSD
Query on HSD

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I [auth A],
J [auth A]
(1S,2S,3R,6R)-6-amino-4-(hydroxymethyl)cyclohex-4-ene-1,2,3-triol
C7 H13 N O4
XPHOBMULWMGEBA-JWXFUTCRSA-N
PCA
Query on PCA

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K [auth A]PYROGLUTAMIC ACID
C5 H7 N O3
ODHCTXKNWHHXJC-VKHMYHEASA-N
SO4
Query on SO4

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H [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

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F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

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G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.379α = 90
b = 74.529β = 90
c = 135.743γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-04
    Changes: Data collection
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Derived calculations, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 3.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary