9OGO | pdb_00009ogo

Crystal Structure of KPT185 in complex with CRM1(EH mutant)-Ran-RanBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

SINE compounds activate exportin 1 degradation through an allosteric mechanism.

Wing, C.E.Fung, H.Y.J.Kwanten, B.Cagatay, T.Niesman, A.B.Jacquemyn, M.Gharghabi, M.Permentier, B.Shakya, B.Nandi, R.Ready, J.M.Kashyap, T.Shacham, S.Landesman, Y.Lapalombella, R.Daelemans, D.Chook, Y.M.

(2025) Nat Chem Biol 21: 2002-2013

  • DOI: https://doi.org/10.1038/s41589-025-02058-0
  • Primary Citation Related Structures: 
    9OG9, 9OGA, 9OGB, 9OGC, 9OGD, 9OGE, 9OGF, 9OGN, 9OGO

  • PubMed Abstract: 

    Overexpression of exportin 1 (XPO1/CRM1) in cancer cells mislocalizes numerous cancer-related nuclear export cargoes. Covalent selective inhibitors of nuclear export (SINEs), including the cancer drug selinexor, restore proper nuclear localization by blocking XPO1-cargo interaction. These inhibitors also induce XPO1 degradation through the Cullin-RING E3 ligase (CRL) substrate receptor ASB8. Here we present cryo-electron microscopy structures revealing ASB8 binding to a cryptic XPO1 site that is exposed upon SINE conjugation. Unlike typical molecular glue degraders that directly bridge CRLs and substrates, SINEs bind XPO1 independently of ASB8, triggering an allosteric mechanism that enables high-affinity ASB8 recruitment, leading to XPO1 ubiquitination and degradation. ASB8-mediated degradation is also triggered by the endogenous itaconate derivative 4-octyl itaconate, suggesting that synthetic XPO1 inhibitors exploit a native cellular mechanism. This allosteric XPO1 degradation mechanism expands known modes of targeted protein degradation beyond molecular glue degraders and proteolysis-targeting chimeras of CRL4.


  • Organizational Affiliation
    • Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 161.8 kDa 
  • Atom Count: 11,276 
  • Modeled Residue Count: 1,333 
  • Deposited Residue Count: 1,404 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran237Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
GTEx:  ENSG00000132341 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62826
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1143Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41920 
Go to UniProtKB:  P41920
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41920
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Exportin-11,024Saccharomyces cerevisiae S288CMutation(s): 4 
Gene Names: CRM1KAP124XPO1YGR218WG8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30822 
Go to UniProtKB:  P30822
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30822
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
(Subject of Investigation/LOI)

Query on GNP



Download:Ideal Coordinates CCD File
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
K85
(Subject of Investigation/LOI)

Query on K85



Download:Ideal Coordinates CCD File
F [auth C]propan-2-yl 3-{3-[3-methoxy-5-(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}propanoate
C16 H18 F3 N3 O3
QJLVYXNWBWLHFD-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.077α = 90
b = 106.077β = 90
c = 303.933γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220582
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP180410
Cancer Prevention and Research Institute of Texas (CPRIT)United States150053
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP170170
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM144137
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM131963
Welch FoundationUnited StatesI-1532

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references
  • Version 1.2: 2026-07-22
    Changes: Database references