Human GLUT1 in complex with Cytochalasin B

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


Mechanism of inhibition of human glucose transporter GLUT1 is conserved between cytochalasin B and phenylalanine amides.

Kapoor, K.Finer-Moore, J.S.Pedersen, B.P.Caboni, L.Waight, A.Hillig, R.C.Bringmann, P.Heisler, I.Muller, T.Siebeneicher, H.Stroud, R.M.

(2016) Proc Natl Acad Sci U S A 113: 4711-4716

  • DOI: https://doi.org/10.1073/pnas.1603735113
  • Primary Citation of Related Structures:  
    5EQG, 5EQH, 5EQI

  • PubMed Abstract: 

    Cancerous cells have an acutely increased demand for energy, leading to increased levels of human glucose transporter 1 (hGLUT1). This up-regulation suggests hGLUT1 as a target for therapeutic inhibitors addressing a multitude of cancer types. Here, we present three inhibitor-bound, inward-open structures of WT-hGLUT1 crystallized with three different inhibitors: cytochalasin B, a nine-membered bicyclic ring fused to a 14-membered macrocycle, which has been described extensively in the literature of hGLUTs, and two previously undescribed Phe amide-derived inhibitors. Despite very different chemical backbones, all three compounds bind in the central cavity of the inward-open state of hGLUT1, and all binding sites overlap the glucose-binding site. The inhibitory action of the compounds was determined for hGLUT family members, hGLUT1-4, using cell-based assays, and compared with homology models for these hGLUT members. This comparison uncovered a probable basis for the observed differences in inhibition between family members. We pinpoint regions of the hGLUT proteins that can be targeted to achieve isoform selectivity, and show that these same regions are used for inhibitors with very distinct structural backbones. The inhibitor cocomplex structures of hGLUT1 provide an important structural insight for the design of more selective inhibitors for hGLUTs and hGLUT1 in particular.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158;

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 2, facilitated glucose transporter member 1492Homo sapiensMutation(s): 0 
Gene Names: SLC2A1GLUT1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P11166 (Homo sapiens)
Explore P11166 
Go to UniProtKB:  P11166
PHAROS:  P11166
GTEx:  ENSG00000117394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11166
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5RH

Download Ideal Coordinates CCD File 
B [auth A]Cytochalasin B
C29 H37 N O5
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.252 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.43α = 90
b = 102.31β = 100.16
c = 68.073γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM024485
Danish Council for Independent ResearchDenmarkDFF-4002-00052
European Research Council (ERC)European Union637372

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2016-05-11
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2020-02-05
    Changes: Structure summary
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description