8WB1 | pdb_00008wb1

Crystal Structure of small molecule KN2H covalently bound to K-Ras(G12D)

• PDB DOI: https://doi.org/10.2210/pdb8WB1/pdb

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


• Deposited: 2023-09-08 Released: 2024-09-11 
• Deposition Author(s): Zhou, L., Zhang, R., Shuai, T.B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Expanding the Chemistry of Acyl Diazo Electrophile as a Tunable Warhead for Covalent Targeting of KRAS (G12D) Mutant.

Shuai, T., Zhang, R., Yuan, Z., Zhang, M., Fan, Z., Ruan, X., Qi, Z., Xie, W., Liu, P., Uesugi, M., Li, Q., Qu, Z., Tan, M., Su, H., Zhou, L.

(2025) J Med Chem 68: 21427-21440

• PubMed: 41017113 
• DOI: https://doi.org/10.1021/acs.jmedchem.5c01365
• Primary Citation Related Structures: 
  8WB1


• PubMed Abstract: 
  

  Covalent warheads are indispensable in the design and development of targeted covalent inhibitors (TCIs). Here, we designed and evaluated acyl diazo probes as an aspartic acid/glutamic acid targeted warhead. Among these probes, P1 demonstrated chemoselectivity for carboxyl residues, even under complex physiological conditions, effectively modifying the proteome in both cell lysates and live cells. Subsequently, we incorporated the warhead onto MRTX-1133, a potent ligand of the KRAS (G12D) mutant, to generate a novel TCI called KN2-H . Compared with other mutants, KN2-H demonstrated covalent modification specifically targeting the KRAS (G12D) mutant, with notable chemoselectivity. It also possessed strong antiproliferative activity against KRAS (G12D) mutant cell lines by downregulating RAS oncogenic signaling. Our findings provide a novel strategy for designing novel TCIs targeting carboxyl residues, based on acyl diazo warheads.

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Organizational Affiliation: 
• School of Pharmacy, Institutes of Biomedical Sciences, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200001, P. R. China.
Department of Hepatobiliary Surgery, Innovative Institute of Tumor Immunity and Medicine (ITIM), Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, P. R. China.
State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, P. R. China.
Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan.
Shanghai Allist Pharmaceuticals Co., Ltd, Shanghai 200001, P. R. China.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 20.56 kDa 
• Atom Count: 1,538 
• Modeled Residue Count: 169 
• Deposited Residue Count: 170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	170	Homo sapiens	Mutation(s): 1  Gene Names: KRAS EC: 3.6.5.2
UniProt
Find proteins for H2Q5M0 (Pan troglodytes) Explore H2Q5M0  Go to UniProtKB:  H2Q5M0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
W3T (Subject of Investigation/LOI)	E [auth A]	1-[(1~{S},5~{R})-3-[7-(8-ethynyl-7-fluoranyl-3-oxidanyl-naphthalen-1-yl)-8-fluoranyl-2-[[(2~{R},8~{S})-2-fluoranyl-1,2,3,5,6,7-hexahydropyrrolizin-8-yl]methoxy]pyrido[4,3-d]pyrimidin-4-yl]-3,8-diazabicyclo[3.2.1]octan-8-yl]ethanone C35 H33 F3 N6 O3 WZSXTLIRLWGGQT-BEOMGMIOSA-N
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.099	α = 90
b = 51.955	β = 90
c = 90.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-09-11 
Deposition Author(s): Zhou, L., Zhang, R., Shuai, T.B.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22077019

Revision History  

• Version 1.0: 2024-09-11
  Type: Initial release
  
• Version 2.0: 2024-10-09
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 2.1: 2026-09-30
  Changes: Database references