3UKR

Crystal structure of Bos taurus Arp2/3 complex with bound inhibitor CK-666


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton.

Baggett, A.W.Cournia, Z.Han, M.S.Patargias, G.Glass, A.C.Liu, S.Y.Nolen, B.J.

(2012) ChemMedChem 7: 1286-1294

  • DOI: 10.1002/cmdc.201200104
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, th ...

    CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, the crystal structure of Arp2/3 complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off-target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its clinical use. Herein we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free-energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a threefold increase in inhibitory activity in vitro relative to 1. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization.


    Organizational Affiliation

    Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 3A418Bos taurusMutation(s): 0 
Gene Names: ACTR3ARP3
Find proteins for P61157 (Bos taurus)
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Go to UniProtKB:  P61157
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2B394Bos taurusMutation(s): 0 
Gene Names: ACTR2ARP2
Find proteins for A7MB62 (Bos taurus)
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Go to UniProtKB:  A7MB62
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 1BC372Bos taurusMutation(s): 0 
Gene Names: ARPC1B
Find proteins for Q58CQ2 (Bos taurus)
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Go to UniProtKB:  Q58CQ2
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 2D300Bos taurusMutation(s): 0 
Gene Names: ARPC2
Find proteins for Q3MHR7 (Bos taurus)
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Go to UniProtKB:  Q3MHR7
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 3E178Bos taurusMutation(s): 0 
Gene Names: ARPC3
Find proteins for Q3T035 (Bos taurus)
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Go to UniProtKB:  Q3T035
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 4F168Bos taurusMutation(s): 0 
Gene Names: ARPC4
Find proteins for Q148J6 (Bos taurus)
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Go to UniProtKB:  Q148J6
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Actin-related protein 2/3 complex subunit 5G151Bos taurusMutation(s): 0 
Gene Names: ARPC5
Find proteins for Q3SYX9 (Bos taurus)
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Go to UniProtKB:  Q3SYX9
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CKH
Query on CKH

Download CCD File 
B
2-fluoro-N-[2-(2-methyl-1H-indol-3-yl)ethyl]benzamide
C18 H17 F N2 O
UXRKUKRXVWJFER-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CKHIC50 :  12000   nM  PDBBind
CKHIC50:  12000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.259 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.186α = 90
b = 129.692β = 90
c = 204.995γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-11-09 
  • Released Date: 2013-02-13 
  • Deposition Author(s): Nolen, B.J., Han, M.

Revision History 

  • Version 1.0: 2013-02-13
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references