7YPZ | pdb_00007ypz

Zafirlukast in complex with CRM1-Ran-RanBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.216 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YPZ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Searching for Novel Noncovalent Nuclear Export Inhibitors through a Drug Repurposing Approach.

Huang, W.Wang, J.X.Shen, X.Lei, Y.Chen, X.Jia, D.Zhang, X.Sun, Q.

(2023) J Med Chem 66: 1574-1582

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01772
  • Primary Citation Related Structures: 
    7YPZ

  • PubMed Abstract: 

    Chromosomal region maintenance protein 1 (CRM1) is a validated anticancer drug target, and its covalent inhibitor KPT-330 has been approved for marketing. However, the development of CRM1 inhibitors, especially the noncovalent ones, is still very limited. Drug repurposing is an effective strategy to develop drug leads for new targets. In this work, we virtually screened a library of marketed drugs and identified zafirlukast as a new CRM1 inhibitor. Biochemical and structural analysis revealed that zafirlukast was a noncovalent CRM1 inhibitor that bound to four subpockets in the nuclear-export-signal (NES) groove. Methylation of the sulfonamide group rendered zafirlukast completely inactive against CRM1. Zafirlukast inhibited the growth of a variety of cancer cells and worked synergistically with the drug doxorubicin. Taken together, these works laid a solid foundation for reshaping zafirlukast as a valuable lead compound for further design of noncovalent, specific, and potent CRM1 inhibitors toward the treatment of various cancers.


  • Organizational Affiliation
    • Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Collaborative Innovation Centre of Biotherapy, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 158.59 kDa 
  • Atom Count: 11,451 
  • Modeled Residue Count: 1,328 
  • Deposited Residue Count: 1,359 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran216Homo sapiensMutation(s): 2 
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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
YRB1 isoform 1140Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1GI526_G0000915
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
CRM1 isoform 11,003Saccharomyces cerevisiaeMutation(s): 11 
Gene Names: CRM1GI526_G0002640PACBIOSEQ_LOCUS2878PACBIOSEQ_LOCUS3002
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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZLK
(Subject of Investigation/LOI)

Query on ZLK



Download:Ideal Coordinates CCD File
BA [auth C]zafirlukast
C31 H33 N3 O6 S
YEEZWCHGZNKEEK-UHFFFAOYSA-N
GTP

Query on GTP



Download:Ideal Coordinates CCD File
J [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MPO

Query on MPO



Download:Ideal Coordinates CCD File
X [auth C]3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
R [auth C],
U [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
S [auth C]
T [auth C]
V [auth C]
E [auth A],
F [auth A],
S [auth C],
T [auth C],
V [auth C],
W [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth C]
G [auth A]
H [auth A]
I [auth A]
L [auth A]
AA [auth C],
G [auth A],
H [auth A],
I [auth A],
L [auth A],
Q [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth A],
M [auth C],
N [auth C],
O [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



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

Query on NA



Download:Ideal Coordinates CCD File
P [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.216 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.782α = 90
b = 105.782β = 90
c = 304.905γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81502629

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Database references
  • Version 1.2: 2026-03-04
    Changes: Refinement description, Structure summary