GDP-bound KRAS G12D in complex with TH-Z816

Experimental Data Snapshot

  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 

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KRAS(G12D) can be targeted by potent inhibitors via formation of salt bridge.

Mao, Z.Xiao, H.Shen, P.Yang, Y.Xue, J.Yang, Y.Shang, Y.Zhang, L.Li, X.Zhang, Y.Du, Y.Chen, C.C.Guo, R.T.Zhang, Y.

(2022) Cell Discov 8: 5-5

  • DOI: https://doi.org/10.1038/s41421-021-00368-w
  • Primary Citation of Related Structures:  
    7EW9, 7EWA, 7EWB

  • PubMed Abstract: 

    KRAS mutation occurs in nearly 30% of human cancers, yet the most prevalent and oncogenic KRAS(G12D) variant still lacks inhibitors. Herein, we designed a series of potent inhibitors that can form a salt bridge with KRAS's Asp12 residue. Our ITC results show that these inhibitors have similar binding affinity with both GDP-bound and GTP-bound KRAS(G12D), and our crystallographic studies reveal the structural basis of inhibitor binding-induced switch-II pocket in KRAS(G12D), experimentally confirming the formation of a salt bridge between the piperazine moiety of the inhibitors and the Asp12 residue of the mutant protein. Among KRAS family proteins and mutants, both ITC and enzymatic assays demonstrate the selectivity of the inhibitors for KRAS(G12D); and the inhibitors disrupt the KRAS-CRAF interaction. We also observed the inhibition of cancer cell proliferation as well as MAPK signaling by a representative inhibitor (TH-Z835). However, since the inhibition was not fully dependent on KRAS mutation status, it is possible that our inhibitors may have off-target effects via targeting non-KRAS small GTPases. Experiments with mouse xenograft models of pancreatic cancer showed that TH-Z835 significantly reduced tumor volume and synergized with an anti-PD-1 antibody. Collectively, our study demonstrates proof-of-concept for a strategy based on salt-bridge and induced-fit pocket formation for KRAS(G12D) targeting, which warrants future medicinal chemistry efforts for optimal efficacy and minimized off-target effects.

  • Organizational Affiliation

    School of Pharmaceutical Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University; Beijing Advanced Innovation Center for Human Brain Protection, Beijing, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2B of GTPase KRas
A, B, C
170Homo sapiensMutation(s): 1 
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
05C (Subject of Investigation/LOI)
Query on 05C

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
C29 H38 N6 O
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C]
C10 H15 N5 O11 P2
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
J [auth C]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.13 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.014α = 90
b = 103.381β = 106.4
c = 56.269γ = 90
Software Package:
Software NamePurpose
SADABSdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81991492

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-29
    Type: Initial release
  • Version 1.1: 2022-07-20
    Changes: Database references, Structure summary
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description