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: 2.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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 kineti ...

    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.,Departments of Biochemistry and Internal Medicine, University of Texas, Southwestern Medical Center, Dallas, TX 75390, USA.,Peloton Therapeutics, Dallas, Texas, a Subsidiary of Merck & Co., Inc., Kenilworth, NJ 07033, USA. Electronic address: xinlin.du@merck.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
1140Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DDB1- and CUL4-associated factor 15
C
498Homo sapiensMutation(s): 0 
Gene Names: DCAF15 (C19orf72)
Find proteins for Q66K64 (Homo sapiens)
Go to Gene View: DCAF15
Go to UniProtKB:  Q66K64
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RNA-binding protein 39
D
109Homo sapiensMutation(s): 0 
Gene Names: RBM39 (HCC1, RNPC2)
Find proteins for Q14498 (Homo sapiens)
Go to Gene View: RBM39
Go to UniProtKB:  Q14498
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DET1- and DDB1-associated protein 1
E
102Homo sapiensMutation(s): 0 
Gene Names: DDA1 (C19orf58, PCIA1)
Find proteins for Q9BW61 (Homo sapiens)
Go to Gene View: DDA1
Go to UniProtKB:  Q9BW61
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
O6M
Query on O6M

Download SDF File 
Download CCD File 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.507α = 90.00
b = 94.767β = 98.06
c = 145.706γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-06-11 
  • Released Date: 2019-09-18 
  • Deposition Author(s): Volkov, O.A., Du, X.

Revision History 

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