5JLJ

Crystal Structure of KPT8602 in complex with CRM1-Ran-RanBP1

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2016-04-27 Released: 2016-06-29 
  • Deposition Author(s): Fung, H.Y., Chook, Y.M.
  • Funding Organization(s): Croucher Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), University of Texas Southwestern Medical Center, Welch Foundation, Leukemia & Lymphoma Society

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Next-generation XPO1 inhibitor shows improved efficacy and in vivo tolerability in hematological malignancies.

Hing, Z.A.Fung, H.Y.Ranganathan, P.Mitchell, S.El-Gamal, D.Woyach, J.A.Williams, K.Goettl, V.M.Smith, J.Yu, X.Meng, X.Sun, Q.Cagatay, T.Lehman, A.M.Lucas, D.M.Baloglu, E.Shacham, S.Kauffman, M.G.Byrd, J.C.Chook, Y.M.Garzon, R.Lapalombella, R.

(2016) Leukemia 30: 2364-2372

  • DOI: https://doi.org/10.1038/leu.2016.136
  • Primary Citation of Related Structures:  
    5JLJ

  • PubMed Abstract: 

    The nuclear export receptor, Exportin 1 (XPO1), mediates transport of growth-regulatory proteins, including tumor suppressors, and is overactive in many cancers, including chronic lymphocytic leukemia (CLL), acute myeloid leukemia (AML) and aggressive lymphomas. Oral selective inhibitor of nuclear export (SINE) compounds that block XPO1 function were recently identified and hold promise as a new therapeutic paradigm in many neoplasms. One of these compounds, KPT-330 (selinexor), has made progress in Phase I/II clinical trials, but systemic toxicities limit its administration to twice-per-week and requiring supportive care. We designed a new generation SINE compound, KPT-8602, with a similar mechanism of XPO1 inhibition and potency but considerably improved tolerability. Efficacy of KPT-8602 was evaluated in preclinical animal models of hematological malignancies, including CLL and AML. KPT-8602 shows similar in vitro potency compared with KPT-330 but lower central nervous system penetration, which resulted in enhanced tolerability, even when dosed daily, and improved survival in CLL and AML murine models compared with KPT-330. KPT-8602 is a promising compound for further development in hematological malignancies and other cancers in which upregulation of XPO1 is seen. The wider therapeutic window of KPT-8602 may also allow increased on-target efficacy leading to even more efficacious combinations with other targeted anticancer therapies.


  • Organizational Affiliation

    Medical Scientist Training Program, The Ohio State University, Columbus, OH, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
PHAROS:  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:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1143Saccharomyces cerevisiae S288CMutation(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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,024Saccharomyces cerevisiae S288CMutation(s): 2 
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
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
6L8
Query on 6L8

Download Ideal Coordinates CCD File 
H [auth C](2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide
C17 H12 F6 N6 O
WXDIWOPYNCJTLO-ZDUSSCGKSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
I [auth C],
J [auth C],
K [auth C],
L [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
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: 2.50 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.929α = 90
b = 105.929β = 90
c = 305.135γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Croucher FoundationHong KongPredoc Scholarship
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP120352, RP150053
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069909
University of Texas Southwestern Medical CenterUnited StatesEndowed Scholars Program
Welch FoundationUnited StatesI-1532
Leukemia & Lymphoma SocietyUnited StatesScholar Award

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-29
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-04-24
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description