5LVX

Crystal structure of glucocerebrosidase with an inhibitory quinazoline modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

beta-Glucocerebrosidase Modulators Promote Dimerization of beta-Glucocerebrosidase and Reveal an Allosteric Binding Site.

Zheng, J.Chen, L.Skinner, O.S.Ysselstein, D.Remis, J.Lansbury, P.Skerlj, R.Mrosek, M.Heunisch, U.Krapp, S.Charrow, J.Schwake, M.Kelleher, N.L.Silverman, R.B.Krainc, D.

(2018) J. Am. Chem. Soc. 140: 5914-5924


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucosylceramidase
A, B, C, D
497Homo sapiensMutation(s): 0 
Gene Names: GBA (GC, GLUC)
EC: 3.2.1.45
Find proteins for P04062 (Homo sapiens)
Go to Gene View: GBA
Go to UniProtKB:  P04062
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
7E4
Query on 7E4

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B, C
11-[(2~{S})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2,3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid
C33 H34 N4 O2
OOVVDXXXFLHSBX-NDEPHWFRSA-N
 Ligand Interaction
79B
Query on 79B

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A, D
11-[(2~{R})-2-[(2-pyridin-3-ylquinazolin-4-yl)amino]-2,3-dihydro-1~{H}-inden-5-yl]undec-10-ynoic acid
C33 H34 N4 O2
OOVVDXXXFLHSBX-MUUNZHRXSA-N
 Ligand Interaction
MAN
Query on MAN

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A, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.910α = 90.00
b = 132.281β = 95.26
c = 103.085γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesR01NS076054

Revision History 

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection
  • Version 1.2: 2018-05-09
    Type: Data collection, Database references
  • Version 1.3: 2018-05-16
    Type: Data collection, Database references
  • Version 1.4: 2018-05-23
    Type: Data collection