9U5T | pdb_00009u5t

GDP-bound KRAS G12D in complex with MCB-294


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.211 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A pan-KRAS inhibitor and its derived degrader elicit multifaceted anti-tumor efficacy in KRAS-driven cancers.

Feng, J.Xiao, X.Xia, X.Min, J.Tang, W.Shi, X.Xu, K.Zhou, G.Li, K.Shen, P.Bao, R.Wu, S.Lin, M.Yuan, K.Lian, Z.Hu, L.Li, N.Wu, Z.Zhai, X.Liu, X.Hu, K.Wu, J.Ding, C.Zhao, H.Gong, X.Zhang, S.Jin, J.Li, D.Liu, M.Ye, Y.Ma, B.Guo, R.T.Zhang, A.Pang, X.

(2025) Cancer Cell 

  • DOI: https://doi.org/10.1016/j.ccell.2025.07.006
  • Primary Citation of Related Structures:  
    9U50, 9U5T, 9USB

  • PubMed Abstract: 

    KRAS remains a challenging therapeutic target with limited effective inhibitors currently available. Here, we report the discovery of MCB-294, a potent dual-state pan-KRAS inhibitor capable of binding both the active (GTP-bound) and inactive (GDP-bound) forms of KRAS. MCB-294 engages the switch-II pocket through a water-mediated hydrogen-bond network and selectively inhibits KRAS over NRAS and HRAS. It effectively suppresses oncogenic KRAS signaling, inhibits the growth of KRAS-dependent cancer cells and patient-derived organoids, and reduces tumor progression in multiple preclinical models. MCB-294 also demonstrates superior activity compared to the inactive-state selective pan-KRAS inhibitor Bl-2865 and the KRAS G12D inhibitor MRTX1133. Building upon MCB-294 as a pan-KRAS-targeting warhead, we further develop MCB-36, a von Hippel-Lindau (VHL)-recruiting pan-KRAS degrader that induces sustained KRAS degradation. Notably, both MCB-294 and MCB-36 effectively suppress KRAS G12C inhibitor-resistant cancer cells and remodel the tumor immune microenvironment. These findings highlight a promising therapeutic strategy for broadly targeting KRAS-driven tumors and overcoming drug resistance.


  • Organizational Affiliation

    Changning Maternity and Infant Health Hospital, Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology and School of Life Sciences, East China Normal University, Shanghai 200241, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas175Homo sapiensMutation(s): 1 
Gene Names: KRASKRAS2RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EN3 (Subject of Investigation/LOI)
Query on A1EN3

Download Ideal Coordinates CCD File 
C [auth A](3~{R})-1-[2-[[(8~{S})-6-[bis(fluoranyl)methylidene]-2,3,5,7-tetrahydro-1~{H}-pyrrolizin-8-yl]methoxy]-7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-pyrido[4,3-d]pyrimidin-4-yl]-3-methyl-piperidin-3-ol
C34 H31 F4 N5 O3
UBTUDOPGKDULSC-NOCHOARKSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.211 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.037α = 90
b = 95.037β = 90
c = 121.012γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SAINTdata scaling
PHASERphasing
REFMACrefinement

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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Database references