7SPS

Crystal structure of human glucose transporter GLUT3 bound with exofacial inhibitor SA47


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for inhibiting human glucose transporters by exofacial inhibitors.

Wang, N.Zhang, S.Yuan, Y.Xu, H.Defossa, E.Matter, H.Besenius, M.Derdau, V.Dreyer, M.Halland, N.He, K.H.Petry, S.Podeschwa, M.Tennagels, N.Jiang, X.Yan, N.

(2022) Nat Commun 13: 2632-2632

  • DOI: https://doi.org/10.1038/s41467-022-30326-3
  • Primary Citation of Related Structures:  
    7SPS, 7SPT

  • PubMed Abstract: 

    Human glucose transporters (GLUTs) are responsible for cellular uptake of hexoses. Elevated expression of GLUTs, particularly GLUT1 and GLUT3, is required to fuel the hyperproliferation of cancer cells, making GLUT inhibitors potential anticancer therapeutics. Meanwhile, GLUT inhibitor-conjugated insulin is being explored to mitigate the hypoglycemia side effect of insulin therapy in type 1 diabetes. Reasoning that exofacial inhibitors of GLUT1/3 may be favored for therapeutic applications, we report here the engineering of a GLUT3 variant, designated GLUT3exo, that can be probed for screening and validating exofacial inhibitors. We identify an exofacial GLUT3 inhibitor SA47 and elucidate its mode of action by a 2.3 Å resolution crystal structure of SA47-bound GLUT3. Our studies serve as a framework for the discovery of GLUTs exofacial inhibitors for therapeutic development.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 2, facilitated glucose transporter member 3
A, B
523Homo sapiensMutation(s): 1 
Gene Names: SLC2A3GLUT3
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P11169 (Homo sapiens)
Explore P11169 
Go to UniProtKB:  P11169
PHAROS:  P11169
GTEx:  ENSG00000059804 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11169
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A0E (Subject of Investigation/LOI)
Query on A0E

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
methyl N-[(2-{4-[4-(5-fluoro-2-methoxyphenyl)piperazin-1-yl]-1H-pyrazolo[3,4-d]pyrimidin-1-yl}phenyl)methyl]-beta-alaninate
C27 H30 F N7 O3
PPQJOTCLVQMNEO-UHFFFAOYSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.591α = 90
b = 121.552β = 108.14
c = 95.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31630017
National Science Foundation (NSF, China)China81861138009
National Science Foundation (NSF, China)China31611130036

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-18
    Type: Initial release
  • Version 1.1: 2022-05-25
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description