6E4L

The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Disruption of endocytosis through chemical inhibition of clathrin heavy chain function.

Dejonghe, W.Sharma, I.Denoo, B.De Munck, S.Lu, Q.Mishev, K.Bulut, H.Mylle, E.De Rycke, R.Vasileva, M.Savatin, D.V.Nerinckx, W.Staes, A.Drozdzecki, A.Audenaert, D.Yperman, K.Madder, A.Friml, J.Van Damme, D.Gevaert, K.Haucke, V.Savvides, S.N.Winne, J.Russinova, E.

(2019) Nat Chem Biol 15: 641-649

  • DOI: 10.1038/s41589-019-0262-1
  • Primary Citation of Related Structures:  
    6E4L

  • PubMed Abstract: 
  • Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acu ...

    Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems.


    Organizational Affiliation

    Center for Plant Systems Biology, VIB, Ghent, Belgium. eurus@psb.vib-ugent.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Clathrin heavy chain 1A369Homo sapiensMutation(s): 0 
Gene Names: CLTCCLH17CLTCL2KIAA0034
Find proteins for Q00610 (Homo sapiens)
Explore Q00610 
Go to UniProtKB:  Q00610
NIH Common Fund Data Resources
PHAROS  Q00610
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HRS
Query on HRS

Download CCD File 
A
5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide
C10 H7 Br N2 O4 S2
XAKPASIXPSBWRB-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.21α = 90
b = 74.34β = 90
c = 84.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references