6PAI

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

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Literature

Structural Basis and Kinetic Pathway of RBM39 Recruitment to DCAF15 by a Sulfonamide Molecular Glue E7820.

Du, X.Volkov, O.A.Czerwinski, R.M.Tan, H.Huerta, C.Morton, E.R.Rizzi, J.P.Wehn, P.M.Xu, R.Nijhawan, D.Wallace, E.M.

(2019) Structure 27: 1625-1633.e3

  • DOI: 10.1016/j.str.2019.10.005
  • Primary Citation of Related Structures:  
    6PAI

  • PubMed Abstract: 
  • E7820 and indisulam are two examples of aryl sulfonamides that recruit RBM39 to Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ligase complex, leading to its ubiquitination and degradation by the proteasome. To understand their mechanism of action, we performed kinetic analysis on the recruitment of RBM39 to DCAF15 and solved a crystal structure of DDA1-DDB1-DCAF15 in complex with E7820 and the RRM2 domain of RBM39 ...

    E7820 and indisulam are two examples of aryl sulfonamides that recruit RBM39 to Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ligase complex, leading to its ubiquitination and degradation by the proteasome. To understand their mechanism of action, we performed kinetic analysis on the recruitment of RBM39 to DCAF15 and solved a crystal structure of DDA1-DDB1-DCAF15 in complex with E7820 and the RRM2 domain of RBM39. E7820 packs in a shallow pocket on the surface of DCAF15 and the resulting modified interface binds RBM39 through the α1 helix of the RRM2 domain. Our kinetic studies revealed that aryl sulfonamide and RBM39 bind to DCAF15 in a synergistic manner. The structural and kinetic studies confirm aryl sulfonamides as molecular glues in the recruitment of RBM39 and provide a framework for future efforts to utilize DCAF15 to degrade other proteins of interest.


    Related Citations: 
    • Structural basis of recruitment of RBM39 to DCAF15 by a sulfonamide molecular glue E7820
      Du, X., Volkov, O.A., Czerwinski, R., Tan, H.L., Huerta, C., Morton, E., Rizzi, J., Wehn, P., Xu, R., Nijhawan, D., Wallace, E.
      (2019) Biorxiv --: --

    Organizational Affiliation

    Peloton Therapeutics, Dallas, Texas, a Subsidiary of Merck & Co., Inc., Kenilworth, NJ 07033, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA damage-binding protein 1A1,140Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
Entity Groups  
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UniProt GroupQ16531
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15B [auth C]498Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
UniProt & NIH Common Fund Data Resources
Find proteins for Q66K64 (Homo sapiens)
Explore Q66K64 
Go to UniProtKB:  Q66K64
PHAROS:  Q66K64
Entity Groups  
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UniProt GroupQ66K64
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-binding protein 39C [auth D]109Homo sapiensMutation(s): 0 
Gene Names: DKFZp781I1140RBM39HCC1RNPC2
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Find proteins for Q14498 (Homo sapiens)
Explore Q14498 
Go to UniProtKB:  Q14498
PHAROS:  Q14498
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UniProt GroupQ14498
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1D [auth E]102Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
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Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
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UniProt GroupQ9BW61
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O6M
Query on O6M

Download Ideal Coordinates CCD File 
G [auth C]3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide
C17 H12 N4 O2 S
LWGUASZLXHYWIV-UHFFFAOYSA-N
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
H [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.507α = 90
b = 94.767β = 98.06
c = 145.706γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-18
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references