6Q6K | pdb_00006q6k

Crystal structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol activity based probe with Cy5 tag (ME569)

PDB DOI: https://doi.org/10.2210/pdb6Q6K/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2018-12-11 Released: 2019-03-27
Deposition Author(s): Rowland, R.J., Davies, G.J.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.221 (Depositor), 0.237 (DCC)
R-Value Work:
0.185 (Depositor), 0.202 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Functionalized Cyclophellitols Are Selective Glucocerebrosidase Inhibitors and Induce a Bona Fide Neuropathic Gaucher Model in Zebrafish.

Artola, M., Kuo, C.L., Lelieveld, L.T., Rowland, R.J., van der Marel, G.A., Codee, J.D.C., Boot, R.G., Davies, G.J., Aerts, J.M.F.G., Overkleeft, H.S.

(2019) J Am Chem Soc 141: 4214-4218

PubMed: 30811188 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.9b00056
Primary Citation Related Structures:
6Q6K, 6Q6L, 6Q6N

PubMed Abstract:
Gaucher disease is caused by inherited deficiency in glucocerebrosidase (GBA, a retaining β-glucosidase), and deficiency in GBA constitutes the largest known genetic risk factor for Parkinson's disease. In the past, animal models of Gaucher disease have been generated by treatment with the mechanism-based GBA inhibitors, conduritol B epoxide (CBE), and cyclophellitol. Both compounds, however, also target other retaining glycosidases, rendering generation and interpretation of such chemical knockout models complicated. Here we demonstrate that cyclophellitol derivatives carrying a bulky hydrophobic substituent at C8 are potent and selective GBA inhibitors and that an unambiguous Gaucher animal model can be readily generated by treatment of zebrafish with these.

Organizational Affiliation

Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom.

Macromolecule Content

Total Structure Weight: 117.57 kDa
Atom Count: 8,992
Modeled Residue Count: 987
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B	497	Homo sapiens	Mutation(s): 0 Gene Names: GBA, GC, GLUC EC: 3.2.1.45 (PDB Primary Data), 3.2.1.46 (UniProt), 2.4.1 (UniProt), 3.2.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P04062 (Homo sapiens) Explore P04062 Go to UniProtKB: P04062
PHAROS: P04062 GTEx: ENSG00000177628
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04062
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P04062-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HKW (Subject of Investigation/LOI) Query on HKW Download:Ideal Coordinates CCD File SDF format, chain AB [auth B] SDF format, chain DA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain DA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain DA [auth A]	AB [auth B], DA [auth A]	6-[3,3-dimethyl-2-[(1~{E},3~{E},5~{E})-5-(1,3,3-trimethylindol-2-ylidene)penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[[1-[[(1~{S},2~{R},3~{R},4~{S},6~{S})-2,3,4,6-tetrakis(oxidanyl)cyclohexyl]methyl]-1,2,3-triazol-4-yl]methyl]hexanamide C₄₂ H₅₅ N₆ O₅ PERJBOWNRMIYFC-ZXMFRAEJSA-O		Interactions Focus chain AB [auth B] Focus chain DA [auth A] Interactions & Density Focus chain AB [auth B] Focus chain DA [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain OA [auth B]	OA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain OA [auth B] Interactions & Density Focus chain OA [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain XA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain XA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain XA [auth B]	AA [auth A] BA [auth A] CA [auth A] N [auth A] O [auth A] AA [auth A], BA [auth A], CA [auth A], N [auth A], O [auth A], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth A] SDF format, chain F [auth A] SDF format, chain FA [auth A] SDF format, chain G [auth A] SDF format, chain GA [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain NA [auth B] MOL2 format, chain BB [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain BB [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B]	BB [auth B] E [auth A] EA [auth A] F [auth A] FA [auth A] BB [auth B], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], NA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B] Interactions & Density Focus chain BB [auth B] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain NA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.221 (Depositor), 0.237 (DCC)
R-Value Work: 0.185 (Depositor), 0.202 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.613	α = 90
b = 285.934	β = 90
c = 92.258	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-27

Deposition Author(s):

Rowland, R.J.

Davies, G.J.

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M011151/1

Revision History (Full details and data files)

Version 1.0: 2019-03-27
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-23
Changes: Structure summary