6OBX | pdb_00006obx

Montbretin A analogue M10-MbA in complex with Human pancreatic alpha-amylase

PDB DOI: https://doi.org/10.2210/pdb6OBX/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-03-21 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: 1.30 Å
R-Value Free:
0.123 (Depositor), 0.120 (DCC)
R-Value Work:
0.099 (Depositor), 0.100 (DCC)
R-Value Observed:
0.100 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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: withers@chem.ubc.ca.

Macromolecule Content

Total Structure Weight: 57.03 kDa
Atom Count: 4,632
Modelled Residue Count: 496
Deposited Residue Count: 496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04746
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P04746-1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZXU Query on ZXU Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-Nalpha-[(2E)-3-(3,4-dihydroxyphenyl )prop-2-enoyl]-L-tyrosinamide C₃₆ H₃₂ N₂ O₁₂ IRVRXEMGBYHLMY-REHZOHHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.123 (Depositor), 0.120 (DCC)
R-Value Work: 0.099 (Depositor), 0.100 (DCC)
R-Value Observed: 0.100 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.42	α = 90
b = 68.22	β = 90
c = 130.33	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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 (Full details and data files)

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: 2024-10-23
Changes: Structure summary