4GPT

Crystal structure of KPT251 in complex with CRM1-Ran-RanBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Antileukemic activity of nuclear export inhibitors that spare normal hematopoietic cells.

Etchin, J.Sun, Q.Kentsis, A.Farmer, A.Zhang, Z.C.Sanda, T.Mansour, M.R.Barcelo, C.McCauley, D.Kauffman, M.Shacham, S.Christie, A.L.Kung, A.L.Rodig, S.J.Chook, Y.M.Look, A.T.

(2013) Leukemia 27: 66-74

  • DOI: 10.1038/leu.2012.219

  • PubMed Abstract: 
  • Drugs that target the chief mediator of nuclear export, chromosome region maintenance 1 protein (CRM1) have potential as therapeutics for leukemia, but existing CRM1 inhibitors show variable potencies and a broad range of cytotoxic effects. Here, we ...

    Drugs that target the chief mediator of nuclear export, chromosome region maintenance 1 protein (CRM1) have potential as therapeutics for leukemia, but existing CRM1 inhibitors show variable potencies and a broad range of cytotoxic effects. Here, we report the structural analysis and antileukemic activity of a new generation of small-molecule inhibitors of CRM1. Designated selective inhibitors of nuclear export (SINE), these compounds were developed using molecular modeling to screen a small virtual library of compounds against the nuclear export signal (NES) groove of CRM1. The 2.2-Å crystal structure of the CRM1-Ran-RanBP1 complex bound to KPT-251, a representative molecule of this class of inhibitors, shows that the drug occupies part of the groove in CRM1 that is usually occupied by the NES, but penetrates much deeper into the groove and blocks CRM1-directed protein export. SINE inhibitors exhibit potent antileukemic activity, inducing apoptosis at nanomolar concentrations in a panel of 14 human acute myeloid leukemia (AML) cell lines representing different molecular subtypes of the disease. When administered orally to immunodeficient mice engrafted with human AML cells, KPT-251 had potent antileukemic activity with negligible toxicity to normal hematopoietic cells. Thus, KPT-SINE CRM1 antagonists represent a novel class of drugs that warrant further testing in AML patients.


    Organizational Affiliation

    Department of Pediatric Oncology, Dana-Farber Cancer Institute, Division of Hematology/Oncology, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
A
216Homo sapiensGene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ran-specific GTPase-activating protein 1
B
140Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: YRB1 (CST20, HTN1, SFO1)
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P41920
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exportin-1
C
1060Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: CRM1 (KAP124, XPO1)
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30822
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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A, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
51K
Query on 51K

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C
2-(2-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}ethyl)-1,3,4-oxadiazole
KPT-251
C14 H9 F6 N5 O
CSKHNYIZBSBQMW-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.165 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.941α = 90.00
b = 105.941β = 90.00
c = 305.480γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4phasing
HKL-2000data scaling
CCP4model building
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-21 
  • Released Date: 2012-09-05 
  • Deposition Author(s): Sun, Q., Chook, Y.M.

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Structure summary
  • Version 1.2: 2013-01-23
    Type: Database references