6OCN

Montbretin A analogue M06-MbA in complex with Human pancreatic alpha-amylase

• PDB DOI: https://doi.org/10.2210/pdb6OCN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): Yes 


• Deposited: 2019-03-25 Released: 2020-02-12 
• Deposition Author(s): Caner, S., Brayer, G.D.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.117 
• R-Value Work: 0.099 
• R-Value Observed: 0.100 

Starting Model: experimental

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5E0F 4W93 5U3A

Literature

Synthesis of montbretin A analogues yields potent competitive inhibitors of human pancreatic alpha-amylase.

Tysoe, C.R., Caner, S., Calvert, M.B., Win-Mason, A., Brayer, G.D., Withers, S.G.

(2019) Chem Sci 10: 11073-11077

• PubMed: 32206255 
• DOI: https://doi.org/10.1039/c9sc02610j
• Primary Citation of Related Structures:  
  6OBX, 6OCN


• PubMed Abstract: 
  

  Simplified analogues of the potent human amylase inhibitor montbretin A were synthesised and shown to bind tightly, K _I = 60 and 70 nM, with improved specificity over medically relevant glycosidases, making them promising candidates for controlling blood glucose. Crystallographic analysis confirmed similar binding modes and identified new active site interactions.

---

Organizational Affiliation: 

Department of Chemistry , University of British Columbia , 2036 Main Mall , Vancouver BC , Canada V6T 1Z1 . Email: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.85 kDa 
• Atom Count: 4,664 
• Modelled Residue Count: 496 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(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
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P04746-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZXY	C [auth A]	N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-1-[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]-L-prolinamide C32 H30 N2 O11 MYJPTGWVMBCTRI-MRSBXDGLSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.15 Å
• R-Value Free: 0.117 
• R-Value Work: 0.099 
• R-Value Observed: 0.100 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.31	α = 90
b = 68.02	β = 90
c = 130.53	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-12 
Deposition Author(s): Caner, S., Brayer, G.D.

---

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR MOP-111082

Revision History  

• Version 1.0: 2020-02-12
  Type: Initial release
  
• Version 1.1: 2020-04-15
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-06
  Changes: Structure summary