9FSH | pdb_00009fsh

Crystal structure of the HECT domain of Smurf 2 in complex with inhibitor 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 
    0.259 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FSH

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Therapeutic potential of allosteric HECT E3 ligase inhibition.

Rothman, A.M.K.Florentin, A.Zink, F.Quigley, C.Bonneau, O.Hemmig, R.Hachey, A.Rejtar, T.Thaker, M.Jain, R.Huang, S.M.Sutton, D.Roger, J.Zhang, J.H.Weiler, S.Cotesta, S.Ottl, J.Srivastava, S.Kordonsky, A.Avishid, R.Yariv, E.Rathi, R.Khvalevsky, O.Troxler, T.Binmahfooz, S.K.Kleifeld, O.Morrell, N.W.Humbert, M.Thomas, M.J.Jarai, G.Beckwith, R.E.J.Cobb, J.S.Smith, N.Ostermann, N.Tallarico, J.Shaw, D.Guth-Gundel, S.Prag, G.Rowlands, D.J.

(2025) Cell 188: 2603

  • DOI: https://doi.org/10.1016/j.cell.2025.03.001
  • Primary Citation Related Structures: 
    9FSH, 9FSJ, 9FSK

  • PubMed Abstract: 

    Targeting ubiquitin E3 ligases is therapeutically attractive; however, the absence of an active-site pocket impedes computational approaches for identifying inhibitors. In a large, unbiased biochemical screen, we discover inhibitors that bind a cryptic cavity distant from the catalytic cysteine of the homologous to E6-associated protein C terminus domain (HECT) E3 ligase, SMAD ubiquitin regulatory factor 1 (SMURF1). Structural and biochemical analyses and engineered escape mutants revealed that these inhibitors restrict an essential catalytic motion by extending an α helix over a conserved glycine hinge. SMURF1 levels are increased in pulmonary arterial hypertension (PAH), a disease caused by mutation of bone morphogenetic protein receptor-2 (BMPR2). We demonstrated that SMURF1 inhibition prevented BMPR2 ubiquitylation, normalized bone morphogenetic protein (BMP) signaling, restored pulmonary vascular cell homeostasis, and reversed pathology in established experimental PAH. Leveraging this deep mechanistic understanding, we undertook an in silico machine-learning-based screen to identify inhibitors of the prototypic HECT E6AP and confirmed glycine-hinge-dependent allosteric activity in vitro. Inhibiting HECTs and other glycine-hinge proteins opens a new druggable space.


  • Organizational Affiliation
    • University of Sheffield, Sheffield, UK; Novartis BioMedical Research (NBR), Cambridge, MA, USA. Electronic address: a.rothman@sheffield.ac.uk.

Macromolecule Content 

  • Total Structure Weight: 58.67 kDa 
  • Atom Count: 3,338 
  • Modeled Residue Count: 373 
  • Deposited Residue Count: 499 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase SMURF2499Homo sapiensMutation(s): 0 
Gene Names: SMURF2
EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAU4 (Homo sapiens)
Explore Q9HAU4 
Go to UniProtKB:  Q9HAU4
PHAROS:  Q9HAU4
GTEx:  ENSG00000108854 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HAU4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TJQ
(Subject of Investigation/LOI)

Query on TJQ



Download:Ideal Coordinates CCD File
B [auth A]ethyl 5-[1,3-benzodioxol-5-ylmethyl(ethyl)carbamoyl]-2,4-dimethyl-1~{H}-pyrrole-3-carboxylate
C20 H24 N2 O5
MTVMTCROAUSHKU-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free:  0.259 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.531α = 90
b = 71.75β = 90
c = 152.624γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Database references