4GMI

BACE-1 in complex with HEA-type macrocyclic inhibitor, MV078571

• PDB DOI: https://doi.org/10.2210/pdb4GMI/pdb

• Classification: Hydrolase/Hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-08-16 Released: 2013-09-04 
• Deposition Author(s): Lindberg, J.D., Derbyshire, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 

Literature

Design and synthesis of novel BACE-1 inhibitors

Sandgren, V., Belda, O., Johansson, P.O., Kvarnstrom, I., Lindberg, J., Dahlgren, A., Samuelsson, B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 44.26 kDa 
• Atom Count: 3,567 
• Modelled Residue Count: 380 
• Deposited Residue Count: 391 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-secretase 1	A	391	Homo sapiens	Mutation(s): 0  Gene Names: BACE1, BACE, KIAA1149 EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens) Explore P56817  Go to UniProtKB:  P56817
PHAROS:  P56817 GTEx:  ENSG00000186318

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XA	B [auth A]	(4S,8E)-4-[(1R)-2-{[2-(5-tert-butyl-1,3-oxazol-2-yl)propan-2-yl]amino}-1-hydroxyethyl]-16-methyl-6-oxa-3-azabicyclo[12.3.1]octadeca-1(18),8,14,16-tetraene-2,13-dione C29 H41 N3 O5 PYRAVCNCGMDZRY-BDCWSOESSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.201 
• R-Value Work: 0.158 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.159	α = 90
b = 76.672	β = 90
c = 104.135	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Lindberg, J.D., Derbyshire, D.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary