6KX2

Crystal structure of GDP bound RhoA protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Covalent Inhibitors Allosterically Block the Activation of Rho Family Proteins and Suppress Cancer Cell Invasion.

Sun, Z.Zhang, H.Zhang, Y.Liao, L.Zhou, W.Zhang, F.Lian, F.Huang, J.Xu, P.Zhang, R.Lu, W.Zhu, M.Tao, H.Yang, F.Ding, H.Chen, S.Yue, L.Zhou, B.Zhang, N.Tan, M.Jiang, H.Chen, K.Liu, B.Liu, C.Dang, Y.Luo, C.

(2020) Adv Sci (Weinh) 7: 2000098-2000098

  • DOI: https://doi.org/10.1002/advs.202000098
  • Primary Citation of Related Structures:  
    6KX2, 6KX3

  • PubMed Abstract: 

    The Rho family GTPases are crucial drivers of tumor growth and metastasis. However, it is difficult to develop GTPases inhibitors due to a lack of well-characterized binding pockets for compounds. Here, through molecular dynamics simulation of the RhoA protein, a groove around cysteine 107 (Cys107) that is relatively well-conserved within the Rho family is discovered. Using a combined strategy, the novel inhibitor DC-Rhoin is discovered, which disrupts interaction of Rho proteins with guanine nucleotide exchange factors (GEFs) and guanine nucleotide dissociation inhibitors (GDIs). Crystallographic studies reveal that the covalent binding of DC-Rhoin to the Cys107 residue stabilizes and captures a novel allosteric pocket. Moreover, the derivative compound DC-Rhoin04 inhibits the migration and invasion of cancer cells, through targeting this allosteric pocket of RhoA. The study reveals a novel allosteric regulatory site within the Rho family, which can be exploited for anti-metastasis drug development, and also provides a novel strategy for inhibitor discovery toward "undruggable" protein targets.


  • Organizational Affiliation

    School of Life Science and Technology Harbin Institute of Technology Harbin 150001 China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein RhoA181Homo sapiensMutation(s): 4 
Gene Names: RHOAARH12ARHARHO12
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens)
Explore P61586 
Go to UniProtKB:  P61586
PHAROS:  P61586
GTEx:  ENSG00000067560 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61586
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.819α = 90
b = 91.819β = 90
c = 56.861γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description