Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen)

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Insights Into the Allosteric Inhibition of the SUMO E2 Enzyme Ubc9.

Hewitt, W.M.Lountos, G.T.Zlotkowski, K.Dahlhauser, S.D.Saunders, L.B.Needle, D.Tropea, J.E.Zhan, C.Wei, G.Ma, B.Nussinov, R.Waugh, D.S.Schneekloth, J.S.

(2016) Angew Chem Int Ed Engl 55: 5703-5707

  • DOI: https://doi.org/10.1002/anie.201511351
  • Primary Citation of Related Structures:  
    5F6D, 5F6E, 5F6U, 5F6V, 5F6W, 5F6X, 5F6Y

  • PubMed Abstract: 

    Conjugation of the small ubiquitin-like modifier (SUMO) to protein substrates is an important disease-associated posttranslational modification, although few inhibitors of this process are known. Herein, we report the discovery of an allosteric small-molecule binding site on Ubc9, the sole SUMO E2 enzyme. An X-ray crystallographic screen was used to identify two distinct small-molecule fragments that bind to Ubc9 at a site distal to its catalytic cysteine. These fragments and related compounds inhibit SUMO conjugation in biochemical assays with potencies of 1.9-5.8 mm. Mechanistic and biophysical analyses, coupled with molecular dynamics simulations, point toward ligand-induced rigidification of Ubc9 as a mechanism of inhibition.

  • Organizational Affiliation

    Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUMO-conjugating enzyme UBC9157Homo sapiensMutation(s): 3 
Gene Names: UBE2IUBC9UBCE9
EC: 6.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63279 (Homo sapiens)
Explore P63279 
Go to UniProtKB:  P63279
GTEx:  ENSG00000103275 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63279
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5VM

Download Ideal Coordinates CCD File 
B [auth A]5-chloranyl-3~{H}-1,3-benzoxazole-2-thione
C7 H4 Cl N O S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.48α = 90
b = 35.558β = 111.64
c = 58.11γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-04
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description