4G55

Clathrin terminal domain complexed with pitstop 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Role of the clathrin terminal domain in regulating coated pit dynamics revealed by small molecule inhibition.

von Kleist, L.Stahlschmidt, W.Bulut, H.Gromova, K.Puchkov, D.Robertson, M.J.MacGregor, K.A.Tomilin, N.Tomlin, N.Pechstein, A.Chau, N.Chircop, M.Sakoff, J.von Kries, J.P.Saenger, W.Krausslich, H.G.Shupliakov, O.Robinson, P.J.McCluskey, A.Haucke, V.

(2011) Cell 146: 471-484

  • DOI: https://doi.org/10.1016/j.cell.2011.06.025
  • Primary Citation of Related Structures:  
    2XZG, 4G55

  • PubMed Abstract: 

    Clathrin-mediated endocytosis (CME) regulates many cell physiological processes such as the internalization of growth factors and receptors, entry of pathogens, and synaptic transmission. Within the endocytic network, clathrin functions as a central organizing platform for coated pit assembly and dissociation via its terminal domain (TD). We report the design and synthesis of two compounds named pitstops that selectively block endocytic ligand association with the clathrin TD as confirmed by X-ray crystallography. Pitstop-induced inhibition of clathrin TD function acutely interferes with receptor-mediated endocytosis, entry of HIV, and synaptic vesicle recycling. Endocytosis inhibition is caused by a dramatic increase in the lifetimes of clathrin coat components, including FCHo, clathrin, and dynamin, suggesting that the clathrin TD regulates coated pit dynamics. Pitstops provide new tools to address clathrin function in cell physiology with potential applications as inhibitors of virus and pathogen entry and as modulators of cell signaling.


  • Organizational Affiliation

    Institute of Chemistry and Biochemistry & Neurocure Cluster of Excellence, Freie Universität Berlin, 14195 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Clathrin heavy chain 1369Homo sapiensMutation(s): 0 
Gene Names: CLH17CLTCCLTCL2KIAA0034
UniProt & NIH Common Fund Data Resources
Find proteins for Q00610 (Homo sapiens)
Explore Q00610 
Go to UniProtKB:  Q00610
PHAROS:  Q00610
GTEx:  ENSG00000141367 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00610
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VH2
Query on VH2

Download Ideal Coordinates CCD File 
S [auth A]N-[5-[(4-BROMOPHENYL)METHYL]-4-HYDROXY-1,3-THIAZOL-2-YL]NAPHTHALENE-1-SULFONAMIDE
C20 H15 Br N2 O3 S2
ULFLIVGUMGQSSF-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth A],
L [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
P [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth A]
N [auth A]
O [auth A]
I [auth A],
J [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A],
R [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
VH2 PDBBind:  4G55 IC50: 1.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.899α = 90
b = 74.019β = 90
c = 82.118γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-01
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Other
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations