29MM | pdb_000029mm

Crystal structure of SHP2 in complex with I-0436650


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.288 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.234 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery and Preclinical Characterization of I-0436650, a Selective SHP2 Allosteric Inhibitor for RAS-Driven Cancers.

Ciammaichella, A.Puca, F.Fabbrini, D.Randazzo, P.Rossetti, I.Sferrazza, A.Ferrigno, F.Grillo, A.Torrente, E.Iaccarino, C.Amaudrut, J.Cellucci, A.Di Marco, A.Palombo, S.Esposito, S.Bisbocci, M.Orsale, M.V.Nibbio, M.Missineo, A.Scalabri, F.Fodale, V.Pucci, V.Alli, C.Di Fabio, R.Montalbetti, C.Carugo, A.Toniatti, C.Petrocchi, A.

(2026) J Med Chem 69: 18898-18914

  • DOI: https://doi.org/10.1021/acs.jmedchem.6c01182
  • Primary Citation Related Structures: 
    29MM

  • PubMed Abstract: 

    SHP2 (Src homology 2 (SH2)-containing protein tyrosine phosphatase 2) is a tyrosine phosphatase that plays a critical role in numerous physiological and pathological cellular processes, including cell proliferation, survival, and migration through the regulation of multiple signaling pathways, such as RAS-RAF-mitogen-activated protein kinase, phosphatidylinositol 3-kinase (PI3K)-AKT, Janus tyrosine kinase (JAK), and signal transducer and activator of transcription pathways (STAT) in response to cytokines and growth factors. Through extensive structure-based optimization, we identified I-0436650, a preclinical candidate with an excellent pharmacological profile. I-0436650 is a low nanomolar allosteric inhibitor of human wild-type (wt) SHP2 and strongly inhibits ERK phosphorylation in cells. It exhibits antiproliferative activity in EGFR- and RAS-dependent cell lines, suppresses tumor growth as a single agent in xenograft models, and delays tumor relapse when combined with inhibitors of the same pathway, demonstrating the potential of vertical inhibition strategies.


  • Organizational Affiliation
    • IRBM S.P.A. Via Pontina Km 30.600, 00071PomeziaRome, Italy.

Macromolecule Content 

  • Total Structure Weight: 121.77 kDa 
  • Atom Count: 8,709 
  • Modeled Residue Count: 996 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 11
A, B
526Homo sapiensMutation(s): 0 
Gene Names: PTPN11PTP2CSHPTP2
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06124
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1J30
(Subject of Investigation/LOI)

Query on A1J30



Download:Ideal Coordinates CCD File
C [auth A],
F [auth B]
(4S)-1'-[5-(3-chloranyl-2-pyrazol-1-yl-pyridin-4-yl)sulfanylpyrazin-2-yl]spiro[4,6-dihydropyrrolo[1,2-b]pyrazole-5,4'-piperidine]-4-amine
C22 H22 Cl N9 S
VUJLHBJEBKDVNJ-HXUWFJFHSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
G [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
E [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.288 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.234 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.517α = 90
b = 213.686β = 96.496
c = 55.896γ = 90
Software Package:
Software NamePurpose
autoPROCdata processing
Aimlessdata scaling
TRUNCATEdata processing
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-08-26
    Changes: Database references