3DXK

Structure of Bos Taurus Arp2/3 Complex with Bound Inhibitor CK0944636


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Literature

Characterization of two classes of small molecule inhibitors of Arp2/3 complex

Nolen, B.J.Tomasevic, N.Russell, A.Pierce, D.W.Jia, Z.McCormick, C.D.Hartman, J.Sakowicz, R.Pollard, T.D.

(2009) Nature 460: 1031-1034

  • DOI: https://doi.org/10.1038/nature08231
  • Primary Citation of Related Structures:  
    3DXK, 3DXM

  • PubMed Abstract: 

    Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells. Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments. CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation. CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation. Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes. Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells.


  • Organizational Affiliation

    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 3418Bos taurusMutation(s): 0 
UniProt
Find proteins for P61157 (Bos taurus)
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UniProt GroupP61157
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2394Bos taurusMutation(s): 0 
UniProt
Find proteins for A7MB62 (Bos taurus)
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UniProt GroupA7MB62
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 1B372Bos taurusMutation(s): 0 
UniProt
Find proteins for Q58CQ2 (Bos taurus)
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UniProt GroupQ58CQ2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 2300Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3MHR7 (Bos taurus)
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UniProt GroupQ3MHR7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 3178Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3T035 (Bos taurus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 4168Bos taurusMutation(s): 0 
UniProt
Find proteins for Q148J6 (Bos taurus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Actin-related protein 2/3 complex subunit 5151Bos taurusMutation(s): 0 
UniProt
Find proteins for Q3SYX9 (Bos taurus)
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N23
Query on N23

Download Ideal Coordinates CCD File 
H [auth B]N-[2-(2-methyl-1H-indol-3-yl)ethyl]thiophene-2-carboxamide
C16 H16 N2 O S
ACAKNPKRLPMONU-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
N23 PDBBind:  3DXK Kd: 470 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.598α = 90
b = 130.657β = 90
c = 203.961γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description