7CRZ | pdb_00007crz

Crystal structure of human glucose transporter GLUT3 bound with C3361


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7CRZ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Orthosteric-allosteric dual inhibitors of PfHT1 as selective antimalarial agents.

Huang, J.Yuan, Y.Zhao, N.Pu, D.Tang, Q.Zhang, S.Luo, S.Yang, X.Wang, N.Xiao, Y.Zhang, T.Liu, Z.Sakata-Kato, T.Jiang, X.Kato, N.Yan, N.Yin, H.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2017749118
  • Primary Citation Related Structures: 
    7CRZ

  • PubMed Abstract: 

    Artemisinin-resistant malaria parasites have emerged and have been spreading, posing a significant public health challenge. Antimalarial drugs with novel mechanisms of action are therefore urgently needed. In this report, we exploit a "selective starvation" strategy by inhibiting Plasmodium falciparum hexose transporter 1 (PfHT1), the sole hexose transporter in P. falciparum , over human glucose transporter 1 (hGLUT1), providing an alternative approach to fight against multidrug-resistant malaria parasites. The crystal structure of hGLUT3, which shares 80% sequence similarity with hGLUT1, was resolved in complex with C3361, a moderate PfHT1-specific inhibitor, at 2.3-Å resolution. Structural comparison between the present hGLUT3-C3361 and our previously reported PfHT1-C3361 confirmed the unique inhibitor binding-induced pocket in PfHT1. We then designed small molecules to simultaneously block the orthosteric and allosteric pockets of PfHT1. Through extensive structure-activity relationship studies, the TH-PF series was identified to selectively inhibit PfHT1 over hGLUT1 and potent against multiple strains of the blood-stage P. falciparum Our findings shed light on the next-generation chemotherapeutics with a paradigm-shifting structure-based design strategy to simultaneously target the orthosteric and allosteric sites of a transporter.


  • Organizational Affiliation
    • Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, School of Pharmaceutical Sciences, Tsinghua University,100084 Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 58.95 kDa 
  • Atom Count: 3,916 
  • Modeled Residue Count: 469 
  • Deposited Residue Count: 518 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Solute carrier family 2, facilitated glucose transporter member 3518Homo 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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
F00
(Subject of Investigation/LOI)

Query on F00



Download:Ideal Coordinates CCD File
B [auth A](2S,3R,4S,5R,6R)-6-(hydroxymethyl)-4-undec-10-enoxy-oxane-2,3,5-triol
C17 H32 O6
YZRNUMHABGDGTN-MTSZKFMLSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.212 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.329α = 90
b = 118.248β = 103.54
c = 54.252γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description