9TKT | pdb_00009tkt

Mapping the SHP2 allosteric pocket with target-biased covalent fragments

• PDB DOI: https://doi.org/10.2210/pdb9TKT/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-12-10 Released: 2026-05-06 
• Deposition Author(s): Roske, Y., Efrem, N.L., Nazare, M., Daumke, O.
• Funding Organization(s): Marie Sklodowska-Curie Actions, FragNET ITN

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.251 (DCC) 

Starting Model: experimental

Literature

Mapping the SHP2 Allosteric Pocket With Target-Biased Covalent Fragments.

Efrem, N.L., Csorba, N., Amoussa, M., Abranyi-Balogh, P., Guo, Z., Petri, L., Bo, F., Di Lorenzo, V., Roske, Y., Szalai, T.V., Mihalovits, L., Simon, J., Li, J., Daumke, O., Keseru, G.M., Nazare, M.

(2026) Chembiochem 27: e70310-e70310

• PubMed: 42033018 
• DOI: https://doi.org/10.1002/cbic.70310
• Primary Citation Related Structures: 
  9TKT


• PubMed Abstract: 
  

  Targeted covalent inhibitors (TCIs) form covalent bonds with a specific amino acid in their target proteins, offering high selectivity and sustained pharmacologic effects. However, identifying optimal electrophilic warheads and nucleophilic amino acids remains a major hurdle for TCI development. While covalent fragment libraries are efficient in the identification of reactive residues, their inherently weak and transient interactions often fail to address functionally relevant binding sites. Here, we combine the exploratory approach of covalent fragment screening with established inhibitor pharmacophores for covalent mapping of the tunnel allosteric site of the oncogenic phosphatase SHP2. Aryl sulfonyl fluoride (SF) fragments featuring pharmacophore elements to enhance noncovalent interactions (target-biased fragments) covalently targeted lysine 492 (K492) in the tunnel binding site, while a conventional SF fragment library lacking these features was not reactive toward K492. Covalent engagement of K492 improved enzyme inhibition and provides a starting point for SHP2 TCI development. More broadly, this study underscores how noncovalent interactions direct covalent fragment binding and highlights target-biased fragments as a complementary strategy to conventional covalent fragment libraries to identify suitable warheads and reactive amino acids in functionally relevant binding sites with minimal a priori knowledge of ligand pharmacophores.

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Organizational Affiliation: 
• Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
Karlsruhe Institute of Technology, Organic Chemistry I, Institute of Organic Chemistry, Karlsruhe, Germany.
Medicinal Chemistry Research Group, HUN-REN Research Centre for Natural Sciences (HUN-REN RCNS), Budapest, Hungary.
National Laboratory for Drug Research and Development, HUN-REN Research Centre for Natural Sciences (HUN-REN RCNS), Budapest, Hungary.
Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.
Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai, China.
Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
Department of Inorganic and Analytical Chemistry, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Budapest, Hungary.
Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Bielefeld, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.81 kDa 
• Atom Count: 8,238 
• Modeled Residue Count: 989 
• Deposited Residue Count: 1,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 11	A, B	524	Homo sapiens	Mutation(s): 0  Gene Names: PTPN11, PTP2C, SHPTP2 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q06124 (Homo sapiens) Explore Q06124  Go to UniProtKB:  Q06124
PHAROS:  Q06124 GTEx:  ENSG00000179295

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JWN (Subject of Investigation/LOI)	E [auth B]	3-[(1~{S})-1-azanylspiro[1,3-dihydroindene-2,4'-piperidine]-1'-yl]carbonylbenzenesulfonic acid C20 H22 N2 O4 S IBCLIJFSBZWNPM-GOSISDBHSA-N
EDO	C [auth B], D [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.283 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.251 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.93	α = 90
b = 212.54	β = 95.23
c = 55.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-06 
Deposition Author(s): Roske, Y., Efrem, N.L., Nazare, M., Daumke, O.

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Funding Organization	Location	Grant Number
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	956314

Revision History  

• Version 1.0: 2026-05-06
  Type: Initial release