9VNG | pdb_00009vng

Small GTPase RhoA Y42C mutant in complex with covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9VNG/pdb

• Classification: CELL INVASION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-06-30 Released: 2026-04-01 
• Deposition Author(s): Wu, H., Jiang, H., Luo, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Discovering Targetable Conformation of RhoA Mutant by Integrating Native Mass Spectrometry, Ultraviolet Photodissociation, and X-ray Diffraction.

Wu, H., Liu, Z., Jiang, H., Zhao, H., Dong, C., Lu, Y., Zu, S., Guo, Y., Lai, C., Luo, P., Xu, K., Yang, Y., Yang, Y., Sun, Z., Huang, Q., Xiong, H., Zhou, L., Luo, Y., Zeng, Y., Du, D., Liang, Z., Xiao, W., Zhao, S., Zhang, W., Tang, Y., Xiao, C., Chen, K., Yang, X., Wang, F., Luo, C.

(2026) J Am Chem Soc 148: 11709-11718

• PubMed: 41837560 
• DOI: https://doi.org/10.1021/jacs.5c20067
• Primary Citation Related Structures: 
  8ZNY, 8ZO0, 9VNG, 9VNH, 9VNI


• PubMed Abstract: 
  

  Pathogenic mutations in "undruggable" Ras superfamily proteins challenge drug development by inducing subtle, dynamic conformational changes. Here, we integrated X-ray crystallography with native mass spectrometry and ultraviolet photodissociation (nMS-UVPD) to reveal a cryptic conformation in the oncogenic Y42C mutant of RhoA. While crystallography alone resolved two ambiguous structures, nMS-UVPD determined the dominant conformation by directly mapping the mutant's conformational dynamics, identifying an enhanced Mg ²⁺ -locked conformation. We explored the mechanism of mutation impairing GTP hydrolysis. This state unmasks a previously hidden, druggable pocket adjacent to Cys42, guiding our identification of a covalent inhibitor. Our integrated approach establishes a roadmap for targeting pathogenic protein mutants previously considered "undruggable" due to their highly dynamic nature.

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Organizational Affiliation: 
• State Key Laboratory of Discovery and Utilization of Functional Components in Traditional Chinese Medicine, Guizhou Medical University, Guiyang 561113, China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
University of Chinese Academy of Sciences, Beijing 100049, China.
State Key Laboratory of Chemical Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China.
School of pharmacy, Fudan University, Shanghai 201203, China.
Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Guangdong 528400, China.
School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.
School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China.
State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Pharmacy and School of Chemical Science and Technology, Yunnan University, Kunming 650500, China.
Southwest United Graduate School, Kunming 650592, China.
Ensem Therapeutics, Inc., 200 Boston Ave., Medford, Massachusetts 02155, United States.
Institute of Advanced Science Facilities, Shenzhen 518107, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.12 kDa 
• Atom Count: 1,519 
• Modeled Residue Count: 172 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A	182	Homo sapiens	Mutation(s): 1  Gene Names: RHOA, ARH12, ARHA, RHO12 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
A1D9L (Subject of Investigation/LOI)	C [auth A]	4-(2-nitroethyl)-1~{H}-indole C10 H10 N2 O2 BPLMVBGQIVJWSL-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.04	α = 90
b = 63.5	β = 90
c = 82.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-04-01 
Deposition Author(s): Wu, H., Jiang, H., Luo, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2026-04-01
  Type: Initial release
  
• Version 1.1: 2026-04-08
  Changes: Database references