8HQ6

KL2 in complex with CRM1-Ran-RanBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Aminoratjadone Derivatives as Potent Noncovalent CRM1 Inhibitors.

Jian, L.Zscherp, R.Beutling, U.Shen, X.Xu, S.Zhang, X.Bronstrup, M.Klahn, P.Sun, Q.

(2023) J Med Chem 66: 11940-11950

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00549
  • Primary Citation of Related Structures:  
    8HQ3, 8HQ6

  • PubMed Abstract: 

    Cancer cells frequently utilize elevated nuclear export to escape tumor suppression and gain proliferative advantage. Chromosome Region Maintenance 1 (CRM1/XPO1) mediates macromolecule nuclear export and plays an important role in tumorigenesis and progression. The clinical approval of its covalent inhibitor KPT-330 (Selinexor) validates the feasibility of targeting CRM1 to treat cancers. Here, we synthesized four aminoratjadone derivatives and found that two of them, KL1 and KL2 , are noncovalent CRM1 inhibitors. The two compounds underwent spontaneous hydrolysis in aqueous buffers, and the resulting products were more active against CRM1. High-resolution crystal structures revealed the CRM1-binding mode of these compounds and explained the observed structure-activity relationships. In cells, KL1 and KL2 localized CRM1 in the nuclear periphery and led to depletion of nuclear CRM1, thereby inhibiting the nuclear export and growth of colorectal cancer cells at submicromolar concentrations. This work lays the foundation for further development of aminoratjadone-based noncovalent CRM1 inhibitors.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
I [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MFF (Subject of Investigation/LOI)
Query on MFF

Download Ideal Coordinates CCD File 
FA [auth C]methyl (3~{S},5~{R},6~{E},8~{Z},10~{R},12~{E},14~{E},16~{S})-3,16-bis(azanyl)-8,10,12-trimethyl-16-[(2~{S},4~{R},5~{S},6~{S})-5-methyl-4-oxidanyl-6-[(~{E})-prop-1-enyl]oxan-2-yl]-5-oxidanyl-hexadeca-6,8,12,14-tetraenoate
C29 H48 N2 O5
PLLUXUKFSITXBR-MOCDELMQSA-N
GLU
Query on GLU

Download Ideal Coordinates CCD File 
K [auth C]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C],
Q [auth C],
Y [auth C],
Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth C],
CA [auth C],
R [auth C],
X [auth C]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
BA [auth C]
DA [auth C]
E [auth A]
EA [auth C]
F [auth A]
BA [auth C],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
H [auth A],
J [auth C],
N [auth C],
P [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
L [auth C],
M [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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.752α = 90
b = 104.752β = 90
c = 302.806γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



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: 2023-10-25
    Type: Initial release