2LK1

Solution structure and binding studies of the RanBP2-type zinc finger of RBM5


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Targeting Zinc Finger Domains with Small Molecules: Solution Structure and Binding Studies of the RanBP2-Type Zinc Finger of RBM5.

Farina, B.Fattorusso, R.Pellecchia, M.

(2011) Chembiochem 12: 2837-2845

  • DOI: https://doi.org/10.1002/cbic.201100582
  • Primary Citation of Related Structures:  
    2LK0, 2LK1

  • PubMed Abstract: 

    The RNA binding motif protein 5 (RBM5), also known as Luca15 or H37, is a component of prespliceosomal complexes that regulates the alternative splicing of several mRNAs, such as Fas and caspase-2. The RBM5 gene is located at the 2p21.3 chromosomal region, which is strongly associated with lung cancer and many other cancers. Both increased and decreased levels of RBM5 can play a role in tumor progression. In particular, downregulation of rbm5 is involved in lung cancer and other cancers upon Ras activation, and, also, represents a molecular signature associated with metastasis in various solid tumors. On the other hand, upregulation of RBM5 occurs in breast and ovarian cancer. Moreover, RBM5 was also found to be involved in the early stage of the HIV-1 viral cycle, representing a potential target for the treatment of the HIV-1 infection. While the molecular basis for RNA recognition and ubiquitin interaction has been structurally characterized, small molecules binding this zinc finger (ZF) domain that might contribute to characterizing their activity and to the development of potential therapeutic agents have not yet been reported. Using an NMR screening of a fragment library we identified several binders and the complex of the most promising one, compound 1, with the RBM5 ZF1 was structurally characterized in solution. Interestingly, the binding mechanism reveals that 1 occupies the RNA binding pocket and is therefore able to compete with the RNA to bind RBM5 RanBP2-type ZF domain, as indicated by NMR studies.


  • Organizational Affiliation

    Infectious Diseases and Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein 532Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P52756 (Homo sapiens)
Explore P52756 
Go to UniProtKB:  P52756
PHAROS:  P52756
GTEx:  ENSG00000003756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52756
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AQN
Query on AQN

Download Ideal Coordinates CCD File 
B [auth A]9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid
C14 H8 O5 S
MMNWSHJJPDXKCH-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AQN PDBBind:  2LK1 Kd: 8.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary