Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 243.18 kDa 
• Atom Count: 17,443 
• Modelled Residue Count: 1,985 
• Deposited Residue Count: 2,144 
• Unique protein chains: 1

 6T13

CRYSTAL STRUCTURE OF GLUCOCEREBROSIDASE IN COMPLEX WITH A PYRROLOPYRAZINE

• PDB DOI:  https://doi.org/10.2210/pdb6T13/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2019-10-03 Released: 2020-12-23 
• Deposition Author(s): Benz, J., Ehler, A., Hug, M., Huber, S., Rufer, A.C., Guba, W., Jagasia, R., Hofmann, E.C., Rodriguez Sarmiento, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Literature

Novel beta-Glucocerebrosidase Activators That Bind to a New Pocket at a Dimer Interface and Induce Dimerization.

Benz, J., Rufer, A.C., Huber, S., Ehler, A., Hug, M., Topp, A., Guba, W., Hofmann, E.C., Jagasia, R., Rodriguez Sarmiento, R.M.

(2021) Angew Chem Int Ed Engl 60: 5436-5442

• PubMed: 33238058 
• DOI: https://doi.org/10.1002/anie.202013890
• Primary Citation of Related Structures:  
  6T13


• PubMed Abstract: 
  

Genetic, preclinical and clinical data link Parkinson's disease and Gaucher's disease and provide a rational entry point to disease modification therapy via enhancement of β-Glucocerebrosidase (GCase) activity. We discovered a new class of pyrrolo[2,3-b]pyrazine activators effecting both Vmax and Km. They bind to human GCase and increase substrate metabolism in the lysosome in a cellular assay. We obtained the first crystal structure for an activator and identified a novel non-inhibitory binding mode at the interface of a dimer, rationalizing the observed structure-activity relationship (SAR). The compound binds GCase inducing formation of a dimeric state at both endoplasmic reticulum (ER) and lysosomal pHs, as confirmed by analytical ultracentrifugation. Importantly, the pyrrolo[2,3-b]pyrazines have central nervous system (CNS) drug-like properties. Our findings are important for future drug discovery efforts in the field of GCase activation and provide a deeper mechanistic understanding of the requirements for enzymatic activation, pointing to the relevance of dimerization.

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Organizational Affiliation: 

Medicinal Chemistry, Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070, Basel, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B, C, D	536	Homo sapiens	Mutation(s): 0  Gene Names: GBA, GC, GLUC EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (UniProt), 3.2.1 (UniProt), 3.2.1.46 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens) Explore P04062  Go to UniProtKB:  P04062
PHAROS:  P04062

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M7H (Subject of Investigation/LOI)	AA [auth C], FA [auth D]	1-[4-[2-(4-methoxyphenyl)-5-methyl-pyrrolo[2,3-b]pyrazin-6-yl]piperidin-1-yl]ethanone C21 H24 N4 O2 HEAGFUMRBLFGAD-UHFFFAOYSA-N
NAG	EA [auth D], N [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	J [auth A], T [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	BA [auth C], CA [auth C], F [auth A], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], JA [auth D], P [auth B], Q [auth B], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	K [auth A], L [auth A], LA [auth D], M [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	DA [auth C], KA [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.849	α = 90
b = 135.408	β = 90
c = 191.384	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XPREP	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-12-23 
Deposition Author(s): Benz, J., Ehler, A., Hug, M., Huber, S., Rufer, A.C., Guba, W., Jagasia, R., Hofmann, E.C., Rodriguez Sarmiento, R.M.

Revision History  

• Version 1.0: 2020-12-23
  Type: Initial release
  
• Version 1.1: 2021-07-21
  Changes: Database references