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9qa5

Structure of the N-SH2 domain of SHP2 in complex with the phosphoY627-Gab1 (613-651) peptide

Method: X-RAY DIFFRACTION Dmax: 44.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Isoform 3 of Tyrosine-protein phosphatase non-receptor type 11

Homo sapiens

UniProt Q06124

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–106 Not recorded GRB2-associated-binding protein 1 × 1 （Q13480） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；5 % PEG3350, 0.2 M NaCl, 0.1 M BisTris, pH 5.5 Resolution 2.08 Å R-free 0.273

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9QA5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2SHP TYROSINE PHOSPHATASE SHP-2 Deposited 1997-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：T2K, F41L, F513S, DEL(528-593) CAT DODECANE-TRIMETHYLAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.00 Å R-free 0.270
2SHP TYROSINE PHOSPHATASE SHP-2 Deposited 1997-12-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：T2K, F41L, F513S, DEL(528-593) CAT DODECANE-TRIMETHYLAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；pH 8.5
Resolution 2.00 Å R-free 0.270
3B7O Crystal structure of the human tyrosine phosphatase SHP2 (PTPN11) with an accessible active site Deposited 2007-10-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 237–529（293 aa） Fragment：;'Residues 237-529 (Isoform 2)' ;
Not recorded MLT D-MALATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 0.15 M Na Malate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.60 Å R-free 0.209
3MOW Crystal structure of SHP2 in complex with a tautomycetin analog TTN D-1 Deposited 2010-04-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 262–532（271 aa） Fragment：CATALYTIC DOMAIN (UNP RESIDUES 262-528)
Not recorded B2B (2Z)-2-[(1R)-3-{[(1R,2S,3R,6S,7S,10S,12S,15E,17E)-18-carboxy-16-ethyl-3,7-dihydroxy-1,2,6,10,12-pentamethyl-5-oxooctade ca-15,17-dien-1-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25% w/v polyethylene glycol 3350, 100 mM sodium chloride, and 100 mM HEPES buffer (pH 7.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.222
3O5X Crystal structure of the oncogenic tyrosine phosphatase SHP2 complexed with a salicylic acid-based small molecule inhibitor Deposited 2010-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 262–532（271 aa） Fragment：UNP RESIDUES 262-532, CATALYTIC DOMAIN
Not recorded JZG 3-{1-[3-(biphenyl-4-ylamino)-3-oxopropyl]-1H-1,2,3-triazol-4-yl}-6-hydroxy-1-methyl-2-phenyl-1H-indole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；20%PEG3350,1%v/v Tacsimate pH7.0, 100mM NaCl, 100 mM HEPES, pH7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.238
3TKZ Structure of the SHP-2 N-SH2 domain in a 1:2 complex with RVIpYFVPLNR peptide Deposited 2011-08-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain (UNP residues 1-106)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3350, 0.1M Bis-Tris, 0.2M Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.80 Å R-free 0.216
3TL0 Structure of SHP2 N-SH2 domain in complex with RLNpYAQLWHR peptide Deposited 2011-08-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain, (UNP residues 1-106)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3350, 0.1 M bis-Tris, 0.2 M Li2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.05 Å R-free 0.234
3ZM0 Catalytic domain of human SHP2 Deposited 2013-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–527（280 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 248-527
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 16-22 % (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE
Resolution 1.50 Å R-free 0.213
3ZM1 Catalytic domain of human SHP2 Deposited 2013-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–527（280 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 248-527
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 16-22% (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE
Resolution 1.40 Å R-free 0.203
3ZM2 Catalytic domain of human SHP2 Deposited 2013-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–527（280 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 248-527
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 16-22% (W/V) PEG3350 0.1-0.2 M SODIUM CITRATE
Resolution 1.50 Å R-free 0.223
3ZM3 Catalytic domain of human SHP2 Deposited 2013-02-04 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 248–531（284 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 248-527
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 16-22% (W/V) PEG3350, 0.1-0.2 M SODIUM CITRATE
Resolution 1.50 Å R-free 0.227
4DGP The wild-type Src homology 2 (SH2)-domain containing protein tyrosine phosphatase-2 (SHP2) Deposited 2012-01-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2, and PTP domains (UNP residues 1-532)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG3350, 300 mM potassium formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.255
4DGX LEOPARD Syndrome-Associated SHP2/Y279C mutant Deposited 2012-01-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2, and PTP domains (UNP residues 1-532)
Mutation：Y279C No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG3350, 300 mM potassium formate, 10 mM calcium chloride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.266
4GWF Crystal structure of the tyrosine phosphatase SHP-2 with Y279C mutation Deposited 2012-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：UNP residues 22-560
Mutation：Y279C EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.1M Tris buffer pH8.0, 15% PEG4000, 0.02M DDT, VAPOR DIFFUSION, temperature 293K
Resolution 2.10 Å R-free 0.243
4GWF Crystal structure of the tyrosine phosphatase SHP-2 with Y279C mutation Deposited 2012-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–543（543 aa） Fragment：UNP residues 22-560
Mutation：Y279C EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.1M Tris buffer pH8.0, 15% PEG4000, 0.02M DDT, VAPOR DIFFUSION, temperature 293K
Resolution 2.10 Å R-free 0.243
4H1O Crystal structure of the tyrosine phosphatase SHP-2 with D61G mutation Deposited 2012-09-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：N-SH2, C-SH2 and Phosphatase domain
Mutation：D61G EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.9；293 K；0.02M DDT, 0.1M Tris pH7.9, 13% PEG4000, 0.1M LiCl , VAPOR DIFFUSION, temperature 293K
Resolution 2.20 Å R-free 0.233
4H34 Crystal structure of the tyrosine phosphatase SHP-2 with Q506P mutation Deposited 2012-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：N-SH2, C-SH2 and Phosphatase domain
Mutation：Q506P EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；0.02M DDT, 0.1M Tris pH8.0, 19% PEG4000, 10% Glycerol, VAPOR DIFFUSION, temperature 293K
Resolution 2.70 Å R-free 0.242
4JE4 Crystal Structure of Monobody NSa1/SHP2 N-SH2 Domain Complex Deposited 2013-02-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–103（103 aa） Fragment：N-terminal SH2 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；30% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium Chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.31 Å R-free 0.255
4JEG Crystal Structure of Monobody CS1/SHP2 C-SH2 Domain Complex Deposited 2013-02-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 97–217（121 aa） Fragment：C-terminal SH2 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG 3350, 0.1M Bis-tris, 0.2M Sodium Chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.227
4JMG Crystal structure of the synthetic protein in complex with pY peptide Deposited 2013-03-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 579–591（13 aa） Fragment：unp residues 579-591
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% (w/v) PEG3000, 0.2 M MgCl2, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 1.40 Å R-free 0.206
4NWF Crystal structure of the tyrosine phosphatase SHP-2 with N308D mutation Deposited 2013-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：UNP residues 1-543
Mutation：N308D EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.6；293 K；13% PEG4000, 0.1M Tris buffer, 10% glycerol, 0.02M DDT, pH 7.6, VAPOR DIFFUSION, temperature 293K
Resolution 2.10 Å R-free 0.309
4NWF Crystal structure of the tyrosine phosphatase SHP-2 with N308D mutation Deposited 2013-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–543（543 aa） Fragment：UNP residues 1-543
Mutation：N308D EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.6；293 K；13% PEG4000, 0.1M Tris buffer, 10% glycerol, 0.02M DDT, pH 7.6, VAPOR DIFFUSION, temperature 293K
Resolution 2.10 Å R-free 0.309
4NWG Crystal structure of the tyrosine phosphatase SHP-2 with E139D mutation Deposited 2013-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–543（543 aa） Fragment：UNP residues 1-543
Mutation：E139D EDO 1,2-ETHANEDIOL × 7 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；14.5% PEG4000, 0.1M Tris buffer, 0.02M DDT, pH 8.0, VAPOR DIFFUSION, temperature 293K
Resolution 2.45 Å R-free 0.326
4NWG Crystal structure of the tyrosine phosphatase SHP-2 with E139D mutation Deposited 2013-12-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–543（543 aa） Fragment：UNP residues 1-543
Mutation：E139D EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；14.5% PEG4000, 0.1M Tris buffer, 0.02M DDT, pH 8.0, VAPOR DIFFUSION, temperature 293K
Resolution 2.45 Å R-free 0.326
4OHD LEOPARD Syndrome-Associated SHP2/A461T mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：A461T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；18% PEG3350, 300 mM KF, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.271
4OHE LEOPARD Syndrome-Associated SHP2/G464A mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：G464A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；20% PEG3350, 300 mM LiCl, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.51 Å R-free 0.256
4OHH LEOPARD Syndrome-Associated SHP2/Q506P mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：Q506P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG3350, 200 mM KF, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.266
4OHI LEOPARD Syndrome-Associated SHP2/Q510E mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：Q510E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；18% PEG3350, 200 mM KF, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.262
4OHL LEOPARD Syndrome-Associated SHP2/T468M mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：T468M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG3350, 300 mM KCOOH, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.259
4OHL LEOPARD Syndrome-Associated SHP2/T468M mutant Deposited 2014-01-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–532（532 aa） Fragment：N-SH2, C-SH2 AND PTP DOMAIN
Mutation：T468M No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；20% PEG3350, 300 mM KCOOH, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.40 Å R-free 0.259
4PVG Crystal structure of protein tyrosine phosphatase Shp2 catalytic domain complex with small molecular compound L88N79 Deposited 2014-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 240–532（293 aa）
Not recorded 2WT 2-[3-({4-[(1,3-benzodioxol-5-ylmethyl)amino]-4-oxobutanoyl}amino)phenyl]-6-hydroxy-3-iodo-1-methyl-1H-indole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；298 K；30% w/v polyethylene glycol 3350, 100 mM NaCl, 1mM L88N79 and 100mM HEPES (pH 7.7) , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.286
4QSY SHP2 SH2 domain in complex with GAB1 peptide Deposited 2014-07-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–106（106 aa） Fragment：SH2 domain, UNP residues 1-104
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG3000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 2.10 Å R-free 0.229
4RDD Co-crystal structure of SHP2 in complex with a Cefsulodin derivative Deposited 2014-09-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 262–532（271 aa） Fragment：SHP2 CATALYTIC DOMAIN
Not recorded 3LU 1-({(2R)-4-carboxy-2-[(R)-carboxy{[(2R)-2-phenyl-2-sulfoacetyl]amino}methyl]-3,6-dihydro-2H-1,3-thiazin-5-yl}methyl)pyridinium × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；293 K；20% PEG3350, 33 mM citric acid, 67 mM BIS-TRIS propane, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.60 Å R-free 0.201
5BK8 Cancer-associated SHP2/T507K mutant Deposited 2019-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Mutation：T507K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG3350, 200 mM LiCl
Resolution 2.25 Å R-free 0.262
5DF6 Crystal structure of PTPN11 tandem SH2 domains in complex with a TXNIP peptide Deposited 2015-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–222（222 aa）
Not recorded UNX UNKNOWN LIGAND × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% PEG-3350, 0.2 M ammonium formate
Resolution 1.78 Å R-free 0.248
5EHP Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP836 Deposited 2015-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：UNP residues 1-525
Not recorded 5OA 5-[2,3-bis(chloranyl)phenyl]-2-[(3~{R},5~{S})-3,5-dimethylpiperazin-1-yl]pyrimidin-4-amine × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG 3350, 200mM Ammonium Phosphate
Resolution 1.85 Å R-free 0.208
5EHP Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP836 Deposited 2015-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：UNP residues 1-525
Not recorded 5OA 5-[2,3-bis(chloranyl)phenyl]-2-[(3~{R},5~{S})-3,5-dimethylpiperazin-1-yl]pyrimidin-4-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG 3350, 200mM Ammonium Phosphate
Resolution 1.85 Å R-free 0.208
5EHR Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099 Deposited 2015-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：UNP residues 1-525
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200mM Ammonium Phosphate
Resolution 1.70 Å R-free 0.221
5EHR Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099 Deposited 2015-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：UNP residues 1-525
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200mM Ammonium Phosphate
Resolution 1.70 Å R-free 0.221
5I6V Structure of F285S, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：F285S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；297 K；0.2M Sodium Malonate, pH7.0, 20% w/v PEG3350
Resolution 1.87 Å R-free 0.232
5I6V Structure of F285S, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：F285S GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；297 K；0.2M Sodium Malonate, pH7.0, 20% w/v PEG3350
Resolution 1.87 Å R-free 0.232
5IBM Structure of S502P, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：S502P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris, 20% PEG 3350 and 1 mM TCEP
Resolution 2.18 Å R-free 0.240
5IBM Structure of S502P, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：S502P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris, 20% PEG 3350 and 1 mM TCEP
Resolution 2.18 Å R-free 0.240
5IBS Structure of E76Q, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：UNP residues 1-525
Mutation：E76Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris, 20% PEG 3350 and 1 mM TCEP
Resolution 2.32 Å R-free 0.238
5IBS Structure of E76Q, a Cancer-Associated Mutation of the Oncogenic Phosphatase SHP2 Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：UNP residues 1-525
Mutation：E76Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris, 20% PEG 3350 and 1 mM TCEP
Resolution 2.32 Å R-free 0.238
5X7B Crystal structure of SHP2_SH2-CagA EPIYA_C peptide complex Deposited 2017-02-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–220（220 aa） Fragment：SH2 (UNP RESIDUES 1-220)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；29%(w/v) PEG4000, 0.1 M Tris-HCl, 0.13 M sodium acetate
Resolution 2.45 Å R-free 0.278
5X94 Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex Deposited 2017-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–220（220 aa） Fragment：SH2 domain (UNP RESIDUES 1-220)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；31% PEG 4000, 0.1 M Tris-HCl
Resolution 2.60 Å R-free 0.246
5X94 Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex Deposited 2017-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–220（220 aa） Fragment：SH2 domain (UNP RESIDUES 1-220)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；31% PEG 4000, 0.1 M Tris-HCl
Resolution 2.60 Å R-free 0.246
5XZR The atomic structure of SHP2 E76A mutant in complex with allosteric inhibitor 9b Deposited 2017-07-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–534（534 aa） Fragment：UNP RESIDUES 1-534
Not recorded 8J6 4-(3-phenylphenyl)-N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3-thiazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Sodium formate, 0.1 M Bicine pH 8.5, 15% w/v PEG 5000MME
Resolution 2.80 Å R-free 0.281
6ATD Oxidized SHP2 forms a disulfide bond between Cys367 and Cys459 Deposited 2017-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–526（526 aa） Fragment：residues 1-526
Mutation：N308D PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；277 K；0.2 M sodium phosphate, 20% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.245
6ATD Oxidized SHP2 forms a disulfide bond between Cys367 and Cys459 Deposited 2017-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–526（526 aa） Fragment：residues 1-526
Mutation：N308D PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；277 K；0.2 M sodium phosphate, 20% (w/v) PEG 3350
Resolution 2.50 Å R-free 0.245
6BMR Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP244 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded DZV 4-[(2-chlorophenyl)methyl]-1-(2-hydroxy-3-methoxyphenyl)[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.21 Å R-free 0.224
6BMR Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP244 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded DZV 4-[(2-chlorophenyl)methyl]-1-(2-hydroxy-3-methoxyphenyl)[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one × 1 PO4 PHOSPHATE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.21 Å R-free 0.224
6BMU Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP244 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DZV 4-[(2-chlorophenyl)methyl]-1-(2-hydroxy-3-methoxyphenyl)[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.12 Å R-free 0.225
6BMU Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP244 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DZV 4-[(2-chlorophenyl)methyl]-1-(2-hydroxy-3-methoxyphenyl)[1,2,4]triazolo[4,3-a]quinazolin-5(4H)-one × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.12 Å R-free 0.225
6BMV Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP504 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded DZS 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2,4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.05 Å R-free 0.223
6BMV Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP504 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded DZS 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2,4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.05 Å R-free 0.223
6BMW Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP504 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DZS 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2,4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.10 Å R-free 0.229
6BMW Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP504 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DZS 3-{4-[(2-chlorophenyl)methyl]-5-oxo-4,5-dihydro[1,2,4]triazolo[4,3-a]quinazolin-1-yl}-4-hydroxybenzoic acid × 1 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.10 Å R-free 0.229
6BMX Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP844 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded DYV 1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1,2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.42 Å R-free 0.252
6BMX Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP844 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded DYV 1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1,2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.42 Å R-free 0.252
6BMY Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DYV 1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1,2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.09 Å R-free 0.228
6BMY Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitors SHP099 and SHP844 Deposited 2017-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 DYV 1-(3-chloro-4-{[1-(2-hydroxy-3-methoxyphenyl)-5-oxo[1,2,4]triazolo[4,3-a]quinazolin-4(5H)-yl]methyl}benzene-1-carbonyl)-L-proline × 1 PO4 PHOSPHATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.09 Å R-free 0.228
6BN5 Non-receptor Protein Tyrosine Phosphatase SHP2 F285S in Complex with Allosteric Inhibitor JLR-2 Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：F285S DZJ 3-benzyl-8-chloro-2-hydroxy-4H-pyrimido[2,1-b][1,3]benzothiazol-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298.15 K；100 mM Tris pH 8.6, 20% PEG 3350, 1 mM TCEP
Resolution 2.22 Å R-free 0.292
6BN5 Non-receptor Protein Tyrosine Phosphatase SHP2 F285S in Complex with Allosteric Inhibitor JLR-2 Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：F285S DZJ 3-benzyl-8-chloro-2-hydroxy-4H-pyrimido[2,1-b][1,3]benzothiazol-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；298.15 K；100 mM Tris pH 8.6, 20% PEG 3350, 1 mM TCEP
Resolution 2.22 Å R-free 0.292
6CMP Closed structure of inactive SHP2 mutant C459E Deposited 2018-03-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–529（529 aa）
Mutation：C459E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM lithium nitrate, 20% PEG 3,350
Resolution 1.80 Å R-free 0.231
6CMP Closed structure of inactive SHP2 mutant C459E Deposited 2018-03-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–529（529 aa）
Mutation：C459E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；200 mM lithium nitrate, 20% PEG 3,350
Resolution 1.80 Å R-free 0.231
6CMQ Structure of human SHP2 without N-SH2 domain Deposited 2018-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 106–529（424 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Resolution 2.90 Å R-free 0.276
6CMQ Structure of human SHP2 without N-SH2 domain Deposited 2018-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 106–529（424 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Resolution 2.90 Å R-free 0.276
6CMQ Structure of human SHP2 without N-SH2 domain Deposited 2018-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 106–529（424 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Resolution 2.90 Å R-free 0.276
6CMQ Structure of human SHP2 without N-SH2 domain Deposited 2018-03-06 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 106–529（424 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；100 mM ammonium formate, 22% PEG 3,350 and 1.5% xylitol
Resolution 2.90 Å R-free 0.276
6CMR Closed structure of active SHP2 mutant E76D bound to SHP099 inhibitor Deposited 2018-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–529（529 aa）
Mutation：E76D 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；15% PEG 20,000 and 10 mM potassium hydrogen tartrate
Resolution 2.21 Å R-free 0.261
6CMS Closed structure of active SHP2 mutant E76K bound to SHP099 inhibitor Deposited 2018-03-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–529（529 aa）
Mutation：E76K 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；291 K；100 mM bicine pH 9, 100 mM NaCl, 19 % PEG MME 550
Resolution 2.68 Å R-free 0.265
6CRF Crystal Structure of Shp2 E76K GOF Mutant in the Open Conformation Deposited 2018-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：E76K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20,000, and 5% Sucrose
Resolution 2.62 Å R-free 0.237
6CRF Crystal Structure of Shp2 E76K GOF Mutant in the Open Conformation Deposited 2018-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：E76K GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M MES pH 6.5, 12% PEG 20,000, and 5% Sucrose
Resolution 2.62 Å R-free 0.237
6CRG Crystal Structure of Shp2 E76K GOF Mutant in complex with SHP099 Deposited 2018-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Mutation：E76K 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Tris pH 8.5, 30% PEG 4000, and 0.2 M LiSO4
Resolution 2.75 Å R-free 0.250
6CRG Crystal Structure of Shp2 E76K GOF Mutant in complex with SHP099 Deposited 2018-03-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Mutation：E76K 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.1 M Tris pH 8.5, 30% PEG 4000, and 0.2 M LiSO4
Resolution 2.75 Å R-free 0.250
6MD7 Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JE1 2-[4-(aminomethyl)-4-methylpiperidin-1-yl]-5-{[2-(trifluoromethyl)pyridin-3-yl]sulfanyl}pyrimidin-4(3H)-one × 1 PO4 PHOSPHATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 1.96 Å R-free 0.209
6MD7 Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrimidinone 7 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JE1 2-[4-(aminomethyl)-4-methylpiperidin-1-yl]-5-{[2-(trifluoromethyl)pyridin-3-yl]sulfanyl}pyrimidin-4(3H)-one × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 1.96 Å R-free 0.209
6MD9 NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WITH ALLOSTERIC INHIBITOR Isoxazolo-pyridinone 3 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JEJ 3-(2-chlorophenyl)-6-{4-[(dimethylamino)methyl]phenyl}-5-methyl[1,2]oxazolo[4,5-c]pyridin-4(5H)-one × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.12 Å R-free 0.272
6MD9 NON-RECEPTOR PROTEIN TYROSINE PHOSPHATASE SHP2 IN COMPLEX WITH ALLOSTERIC INHIBITOR Isoxazolo-pyridinone 3 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JEJ 3-(2-chlorophenyl)-6-{4-[(dimethylamino)methyl]phenyl}-5-methyl[1,2]oxazolo[4,5-c]pyridin-4(5H)-one × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.12 Å R-free 0.272
6MDA Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyridine 4 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JED 3-(4-bromophenyl)-6-(4-methylphenyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.21 Å R-free 0.251
6MDA Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyridine 4 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JED 3-(4-bromophenyl)-6-(4-methylphenyl)-1H-pyrazolo[3,4-b]pyridine-4-carboxylic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.21 Å R-free 0.251
6MDB Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidinone 5 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JE4 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)-5-methyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.34 Å R-free 0.236
6MDB Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidinone 5 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JE4 6-(4-amino-4-methylpiperidin-1-yl)-3-(2,3-dichlorophenyl)-5-methyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.34 Å R-free 0.236
6MDC Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidinone 1 SHP389 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JEA 6-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-[3-chloro-2-(cyclopropylamino)pyridin-4-yl]-5-methyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.14 Å R-free 0.239
6MDC Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Pyrazolo-pyrimidinone 1 SHP389 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JEA 6-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-[3-chloro-2-(cyclopropylamino)pyridin-4-yl]-5-methyl-2,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.14 Å R-free 0.239
6MDD Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Imidazo-pyridine 24 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded JE7 5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.05 Å R-free 0.251
6MDD Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Imidazo-pyridine 24 Deposited 2018-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded JE7 5-[(2,3-dichlorophenyl)sulfanyl]-3H-imidazo[4,5-b]pyridin-2-amine × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；17% PEG3350, 200MM AMMONIUM PHOSPHATE
Resolution 2.05 Å R-free 0.251
6R5G C-SH2 domain of SHP-2 in complex with phospho-ITSM of PD-1 Deposited 2019-03-25 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 105–220（116 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 800 uM [U-13C; U-15N] C-SH2 domain of SHP-2, 1000 uM ITSM, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 800 uM [U-13C; U-15N] C-SH2 domain of SHP-2, 640 uM ITSM, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6ROY Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif Deposited 2019-05-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–104（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；291 K；31.7% (w/v) PEG3350, 0.1 M HEPES, 0.233 M MgSO4
Resolution 2.10 Å R-free 0.279
6ROY Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based inhibitory motif Deposited 2019-05-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 3–104（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；291 K；31.7% (w/v) PEG3350, 0.1 M HEPES, 0.233 M MgSO4
Resolution 2.10 Å R-free 0.279
6ROZ Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based switch motif Deposited 2019-05-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 3–104（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；31.7% (w/v) PEG 3350, 0.1 M HEPES, 0.233 M MgSO4
Resolution 2.89 Å R-free 0.285
6ROZ Structure of the N-SH2 domain of the human tyrosine-protein phosphatase non-receptor type 11 in complex with the phosphorylated immune receptor tyrosine-based switch motif Deposited 2019-05-13 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 3–104（102 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.1；293 K；31.7% (w/v) PEG 3350, 0.1 M HEPES, 0.233 M MgSO4
Resolution 2.89 Å R-free 0.285
6WU8 Structure of human SHP2 in complex with inhibitor IACS-13909 Deposited 2020-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–530（530 aa）
Not recorded U9Y 1-[3-(2,3-dichlorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.40 Å R-free 0.270
6WU8 Structure of human SHP2 in complex with inhibitor IACS-13909 Deposited 2020-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–530（530 aa）
Not recorded U9Y 1-[3-(2,3-dichlorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.40 Å R-free 0.270
7EMN The atomic structure of SHP2 E76A mutant Deposited 2021-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–534（534 aa）
Mutation：E76A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M sodium formate, 0.1 M Bicine ph 8.5, 15% w/v PEG 5000MME
Resolution 3.00 Å R-free 0.271
7EMN The atomic structure of SHP2 E76A mutant Deposited 2021-04-14 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–534（534 aa）
Mutation：E76A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；0.2M sodium formate, 0.1 M Bicine ph 8.5, 15% w/v PEG 5000MME
Resolution 3.00 Å R-free 0.271
7JVM Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TNO155 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded VKS (3S,4S)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；17% PEG 3350 and 200 mM ammonium phosphate
Resolution 2.17 Å R-free 0.236
7JVM Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TNO155 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded VKS (3S,4S)-8-{6-amino-5-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；17% PEG 3350 and 200 mM ammonium phosphate
Resolution 2.17 Å R-free 0.236
7JVN Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Compound 24 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded VKP 6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine × 1 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；17% PEG 3350 and 200 mM ammonium phosphate
Resolution 1.92 Å R-free 0.214
7JVN Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor Compound 24 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded VKP 6-(4-amino-4-methylpiperidin-1-yl)-3-[(2,3-dichlorophenyl)sulfanyl]pyrazin-2-amine × 1 PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；17% PEG 3350 and 200 mM ammonium phosphate
Resolution 1.92 Å R-free 0.214
7PPL SHP2 catalytic domain in complex with IRS1 (625-639) phosphopeptide (pTyr-632, pSer-636) Deposited 2021-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 246–314（69 aa）
Chain A 324–528（205 aa）
Mutation：catalytic inactivation: C213S Mutation：catalytic inactivation: C213S GOL GLYCEROL × 5 EOH ETHANOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG 20000, 100mM HEPES buffer pH 7.5, 50mM EDTA
Resolution 1.53 Å R-free 0.197
7PPM SHP2 catalytic domain in complex with IRS1 (889-901) phosphopeptide (pSer-892, pTyr-896) Deposited 2021-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 246–314（69 aa）
Chain A 324–528（205 aa）
Mutation：catalytic inactivation: C213S Mutation：catalytic inactivation: C213S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；10% PEG 20000, 100mM Citrate buffer pH 5.5, EDTA 50mM
Resolution 1.48 Å R-free 0.196
7PPN SHP2 catalytic domain in complex with CD28 (183-198) phosphopeptide (pTyr-191, p-Thr-195) Deposited 2021-09-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 246–314（69 aa）
Chain A 324–528（205 aa）
Mutation：catalytic inactivation: C213S Mutation：catalytic inactivation: C213S GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；10% PEG 20000, 100 mM Citrate buffer pH 5.5, 50 mM EDTA
Resolution 1.90 Å R-free 0.207
7R75 Structure of human SHP2 in complex with compound 16 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–530（530 aa）
Not recorded 33I 6-(4-amino-4-methylpiperidin-1-yl)-3-(3-chlorophenyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.83 Å R-free 0.289
7R7D Structure of human SHP2 in complex with compound 22 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–530（530 aa）
Not recorded 37I 4-[6-(4-amino-4-methylpiperidin-1-yl)-1H-pyrazolo[3,4-b]pyrazin-3-yl]-3-chloro-N-methylpyridin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.60 Å R-free 0.260
7R7D Structure of human SHP2 in complex with compound 22 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–530（530 aa）
Not recorded 37I 4-[6-(4-amino-4-methylpiperidin-1-yl)-1H-pyrazolo[3,4-b]pyrazin-3-yl]-3-chloro-N-methylpyridin-2-amine × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.60 Å R-free 0.260
7R7I Structure of human SHP2 in complex with compound 27 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–530（530 aa）
Not recorded 3CW [3-(4-amino-4-methylpiperidin-1-yl)-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl]methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.85 Å R-free 0.292
7R7I Structure of human SHP2 in complex with compound 27 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–530（530 aa）
Not recorded 3CW [3-(4-amino-4-methylpiperidin-1-yl)-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl]methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 2.85 Å R-free 0.292
7R7L Structure of human SHP2 in complex with compound 30 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–530（530 aa）
Not recorded 3ED 6-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-(2,3-dichlorophenyl)-2-methylpyrimidin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 3.00 Å R-free 0.286
7R7L Structure of human SHP2 in complex with compound 30 Deposited 2021-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–530（530 aa）
Not recorded 3ED 6-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-3-(2,3-dichlorophenyl)-2-methylpyrimidin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；300 mM potassium formate, 14% w/v PEG3350
Resolution 3.00 Å R-free 0.286
7RCT Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor RMC-4550 Deposited 2021-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 4Q4 {3-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl}methanol × 1 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium Chloride 0.1 M BIS-TRIS propane pH 8.5 11% PEG 1500
Resolution 1.80 Å R-free 0.225
7RCT Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor RMC-4550 Deposited 2021-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 4Q4 {3-[(3S,4S)-4-amino-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-6-(2,3-dichlorophenyl)-5-methylpyrazin-2-yl}methanol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Sodium Chloride 0.1 M BIS-TRIS propane pH 8.5 11% PEG 1500
Resolution 1.80 Å R-free 0.225
7TVJ Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex Deposited 2022-02-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 224–525（302 aa）
Not recorded FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；292 K；0.1 M sodium citrate tribasic dihydrate, 2% Tascimate, 16% PEG3350
Resolution 2.39 Å R-free 0.259
7TVJ Crystal Structure of Monobody Mb(SHP2PTP_13)/SHP2 PTP Domain Complex Deposited 2022-02-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 224–525（302 aa）
Not recorded FLC CITRATE ANION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5；292 K；0.1 M sodium citrate tribasic dihydrate, 2% Tascimate, 16% PEG3350
Resolution 2.39 Å R-free 0.259
7VXG Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453 Deposited 2021-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 83Q 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；295 K；100mM Tris-HCl pH 8.2, 12% (vol/vol) PEG 4000, 20mM DTT
Resolution 2.10 Å R-free 0.325
7VXG Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453 Deposited 2021-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 83Q 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；295 K；100mM Tris-HCl pH 8.2, 12% (vol/vol) PEG 4000, 20mM DTT
Resolution 2.10 Å R-free 0.325
7VXG Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453 Deposited 2021-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–525（525 aa）
Not recorded 83Q 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；295 K；100mM Tris-HCl pH 8.2, 12% (vol/vol) PEG 4000, 20mM DTT
Resolution 2.10 Å R-free 0.325
7VXG Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor TK-453 Deposited 2021-11-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–525（525 aa）
Not recorded 83Q 6-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-3-[2,3-bis(chloranyl)phenyl]sulfanyl-pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；295 K；100mM Tris-HCl pH 8.2, 12% (vol/vol) PEG 4000, 20mM DTT
Resolution 2.10 Å R-free 0.325
7XHQ Small-molecule Allosteric Regulation Mechanism of SHP2 Deposited 2022-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded FIZ 2-[(3S,4R)-4-azanyl-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Tris-HCl, pH 8.5, 13%-18% PEG 4000
Resolution 2.20 Å R-free 0.275
7XHQ Small-molecule Allosteric Regulation Mechanism of SHP2 Deposited 2022-04-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded FIZ 2-[(3S,4R)-4-azanyl-3-methyl-2-oxa-8-azaspiro[4.5]decan-8-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Tris-HCl, pH 8.5, 13%-18% PEG 4000
Resolution 2.20 Å R-free 0.275
8B5Y SHP2 in complex with allosteric imidazopyrazine inhibitor Deposited 2022-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded P8O (1~{S})-1'-[5-[2-(trifluoromethyl)pyridin-3-yl]sulfanyl-3~{H}-imidazo[4,5-b]pyrazin-2-yl]spiro[1,3-dihydroindene-2,4'-piperidine]-1-amine × 1 FMT FORMIC ACID × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；21.00 %w/v PEG 3350, 0.30 M K Form
Resolution 1.83 Å R-free 0.218
8B5Y SHP2 in complex with allosteric imidazopyrazine inhibitor Deposited 2022-09-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded P8O (1~{S})-1'-[5-[2-(trifluoromethyl)pyridin-3-yl]sulfanyl-3~{H}-imidazo[4,5-b]pyrazin-2-yl]spiro[1,3-dihydroindene-2,4'-piperidine]-1-amine × 1 FMT FORMIC ACID × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；21.00 %w/v PEG 3350, 0.30 M K Form
Resolution 1.83 Å R-free 0.218
8CBH SHP2 in complex with a novel allosteric inhibitor Deposited 2023-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded U70 [(1~{S},6~{R},7~{S})-3-[3-[2,3-bis(chloranyl)phenyl]-2~{H}-pyrazolo[3,4-b]pyrazin-6-yl]-7-(4-methyl-1,3-thiazol-2-yl)-3-azabicyclo[4.1.0]heptan-7-yl]methanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293.15 K；14.00 %w/v PEG 3350, 0.20 M NH4 Acetate, 0.10 M Tris pH=9.00
Resolution 2.24 Å R-free 0.264
8CBH SHP2 in complex with a novel allosteric inhibitor Deposited 2023-01-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded U70 [(1~{S},6~{R},7~{S})-3-[3-[2,3-bis(chloranyl)phenyl]-2~{H}-pyrazolo[3,4-b]pyrazin-6-yl]-7-(4-methyl-1,3-thiazol-2-yl)-3-azabicyclo[4.1.0]heptan-7-yl]methanamine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293.15 K；14.00 %w/v PEG 3350, 0.20 M NH4 Acetate, 0.10 M Tris pH=9.00
Resolution 2.24 Å R-free 0.264
8GWW Small-molecule Allosteric Regulation Mechanism of SHP2 Deposited 2022-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded KID 2-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Tris-HCl, pH 8.5, 13%-18% PEG 4000
Resolution 3.00 Å R-free 0.288
8GWW Small-molecule Allosteric Regulation Mechanism of SHP2 Deposited 2022-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded KID 2-[4-(aminomethyl)-4-methyl-piperidin-1-yl]-5-[2,3-bis(chloranyl)phenyl]-3-methyl-pyrrolo[2,1-f][1,2,4]triazin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M Tris-HCl, pH 8.5, 13%-18% PEG 4000
Resolution 3.00 Å R-free 0.288
8RZW A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4N 3,5-bis(chloranyl)pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.02 Å R-free 0.272
8RZW A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4N 3,5-bis(chloranyl)pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.02 Å R-free 0.272
8RZY A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4L 1H-pyrrolo[3,2-b]pyridin-5-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.91 Å R-free 0.220
8RZY A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4L 1H-pyrrolo[3,2-b]pyridin-5-amine × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.91 Å R-free 0.220
8S01 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4J 3-(4-chlorophenyl)-1H-pyrazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.17 Å R-free 0.231
8S01 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4J 3-(4-chlorophenyl)-1H-pyrazole × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.17 Å R-free 0.231
8S04 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4I N-(1H-indol-7-yl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.89 Å R-free 0.223
8S04 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4I N-(1H-indol-7-yl)methanesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.89 Å R-free 0.223
8S06 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4M 1H-pyrrolo[3,2-b]pyridin-7-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.19 Å R-free 0.238
8S06 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4M 1H-pyrrolo[3,2-b]pyridin-7-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.19 Å R-free 0.238
8S07 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded FMT FORMIC ACID × 4 A1H4K 7-azanyl-N-pyridin-3-yl-3H-pyrrolo[3,2-b]pyridine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.83 Å R-free 0.212
8S07 A fragment-based inhibitor of SHP2 Deposited 2024-02-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4K 7-azanyl-N-pyridin-3-yl-3H-pyrrolo[3,2-b]pyridine-2-carboxamide × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.83 Å R-free 0.212
8S0H A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4Q 5-(aminomethyl)-N-(3-chloranyl-1-methyl-indol-7-yl)-1,3-dihydroisoindole-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.99 Å R-free 0.254
8S0H A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4Q 5-(aminomethyl)-N-(3-chloranyl-1-methyl-indol-7-yl)-1,3-dihydroisoindole-2-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.99 Å R-free 0.254
8S0I A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4P 3-phenyl-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.93 Å R-free 0.224
8S0I A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4P 3-phenyl-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.93 Å R-free 0.224
8S0J A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4R 3-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]propan-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.89 Å R-free 0.242
8S0J A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4R 3-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]propan-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.89 Å R-free 0.242
8S0K A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4S 3-[2,3-bis(chloranyl)phenyl]-5-methyl-6-(piperazin-1-ylmethyl)-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.84 Å R-free 0.228
8S0K A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4S 3-[2,3-bis(chloranyl)phenyl]-5-methyl-6-(piperazin-1-ylmethyl)-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.84 Å R-free 0.228
8S0O A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded FMT FORMIC ACID × 1 A1H4G 3-[4-chloranyl-2-(1H-pyrazol-4-ylmethyl)indazol-5-yl]-5-methyl-6-(piperazin-1-ylmethyl)-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.83 Å R-free 0.236
8S0O A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded FMT FORMIC ACID × 1 A1H4G 3-[4-chloranyl-2-(1H-pyrazol-4-ylmethyl)indazol-5-yl]-5-methyl-6-(piperazin-1-ylmethyl)-1H-pyrrolo[3,2-b]pyridine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.83 Å R-free 0.236
8S0P A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4O 1-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]-4-methyl-piperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.00 Å R-free 0.244
8S0P A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4O 1-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]-4-methyl-piperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 2.00 Å R-free 0.244
8S0Q A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4T (1S,5R)-8-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]-8-azabicyclo[3.2.1]octan-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.87 Å R-free 0.236
8S0Q A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4T (1S,5R)-8-[3-[2,3-bis(chloranyl)phenyl]-1H-pyrrolo[3,2-b]pyridin-6-yl]-8-azabicyclo[3.2.1]octan-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.87 Å R-free 0.236
8S0S A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Not recorded A1H4H (1R,5S)-8-[7-(4-chloranyl-2-methyl-indazol-5-yl)-5H-pyrrolo[2,3-b]pyrazin-3-yl]-8-azabicyclo[3.2.1]octan-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.94 Å R-free 0.258
8S0S A fragment-based inhibitor of SHP2 Deposited 2024-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Not recorded A1H4H (1R,5S)-8-[7-(4-chloranyl-2-methyl-indazol-5-yl)-5H-pyrrolo[2,3-b]pyrazin-3-yl]-8-azabicyclo[3.2.1]octan-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.5M K formate 15% PEG 3350 0.1M pH=8 Bis-Tris propane/HCl
Resolution 1.94 Å R-free 0.258
8T6D Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded SO4 SULFATE ION × 5 YR2 (3R)-1'-[3-(3,4-dihydro-1,5-naphthyridin-1(2H)-yl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-3H-spiro[[1]benzofuran-2,4'-piperidin]-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 2.40 Å R-free 0.296
8T6D Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded SO4 SULFATE ION × 4 YR2 (3R)-1'-[3-(3,4-dihydro-1,5-naphthyridin-1(2H)-yl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-3H-spiro[[1]benzofuran-2,4'-piperidin]-3-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 2.40 Å R-free 0.296
8T6G Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded SO4 SULFATE ION × 6 YT2 (1S)-1-{6-[(1S)-1-amino-1,3-dihydrospiro[indene-2,4'-piperidin]-1'-yl]-3-(3,4-dihydro-1,5-naphthyridin-1(2H)-yl)-1H-pyrazolo[3,4-b]pyrazin-5-yl}ethan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 1.84 Å R-free 0.245
8T6G Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded SO4 SULFATE ION × 7 YT2 (1S)-1-{6-[(1S)-1-amino-1,3-dihydrospiro[indene-2,4'-piperidin]-1'-yl]-3-(3,4-dihydro-1,5-naphthyridin-1(2H)-yl)-1H-pyrazolo[3,4-b]pyrazin-5-yl}ethan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 1.84 Å R-free 0.245
8T7Q Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded ZH5 1-{3-[(2-chlorophenyl)sulfanyl]-1H-pyrazolo[3,4-b]pyrazin-6-yl}-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 2.10 Å R-free 0.262
8T7Q Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded ZH5 1-{3-[(2-chlorophenyl)sulfanyl]-1H-pyrazolo[3,4-b]pyrazin-6-yl}-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate
Resolution 2.10 Å R-free 0.262
8T8Q Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded ZJX 1-[(3P)-3-(3-chloro-2-fluorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG3350, 0.3 M Ammonium Sulfate, 0.1 M Tris (pH 8.5)
Resolution 2.27 Å R-free 0.249
8T8Q Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors Deposited 2023-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded ZJX 1-[(3P)-3-(3-chloro-2-fluorophenyl)-1H-pyrazolo[3,4-b]pyrazin-6-yl]-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；19% PEG3350, 0.3 M Ammonium Sulfate, 0.1 M Tris (pH 8.5)
Resolution 2.27 Å R-free 0.249
8U7W Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with inhibitor compound 7 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：residues 1-525
Not recorded W8I 1-{6-[(2,3-dichlorophenyl)sulfanyl]pyrido[2,3-b]pyrazin-2-yl}-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；17% PEG3350, 0.1M Bicine, pH9.2, 30 mM Ammonium Acetate, 4% Tacsimate
Resolution 2.05 Å R-free 0.178
8U7W Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with inhibitor compound 7 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：residues 1-525
Not recorded W8I 1-{6-[(2,3-dichlorophenyl)sulfanyl]pyrido[2,3-b]pyrazin-2-yl}-4-methylpiperidin-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；17% PEG3350, 0.1M Bicine, pH9.2, 30 mM Ammonium Acetate, 4% Tacsimate
Resolution 2.05 Å R-free 0.178
8U7X Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with inhibitor compound 24 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：residues 1-525
Not recorded WAB (3S,4S)-8-{6-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrido[2,3-b]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；13% PEG3350, 0.1M Bicine, pH7.6, 30mM Ammonium Acetate, 5% Tacsimate
Resolution 2.06 Å R-free 0.175
8U7X Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with inhibitor compound 24 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：residues 1-525
Not recorded WAB (3S,4S)-8-{6-[(2-amino-3-chloropyridin-4-yl)sulfanyl]pyrido[2,3-b]pyrazin-2-yl}-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；13% PEG3350, 0.1M Bicine, pH7.6, 30mM Ammonium Acetate, 5% Tacsimate
Resolution 2.06 Å R-free 0.175
8WFY The Crystal Structure of SHP2 from Biortus. Deposited 2023-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% Tryptone, 0.001M NaN3, 0.05M HEPEs-Na pH 7.0, 20% PEG 3350
Resolution 2.60 Å R-free 0.317
8WFY The Crystal Structure of SHP2 from Biortus. Deposited 2023-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded 5OD 6-(4-azanyl-4-methyl-piperidin-1-yl)-3-[2,3-bis(chloranyl)phenyl]pyrazin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1% Tryptone, 0.001M NaN3, 0.05M HEPEs-Na pH 7.0, 20% PEG 3350
Resolution 2.60 Å R-free 0.317
8WX7 Crystal structure of SHP2 in complex with JAB-3186 Deposited 2023-10-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 XD8 (5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine × 1 SO4 SULFATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulphate, 28 % w/v PEG3350
Resolution 2.02 Å R-free 0.246
8WX7 Crystal structure of SHP2 in complex with JAB-3186 Deposited 2023-10-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 XD8 (5~{S})-1'-[6-azanyl-5-(2-azanyl-3-chloranyl-pyridin-4-yl)sulfanyl-pyrazin-2-yl]spiro[5,7-dihydrocyclopenta[b]pyridine-6,4'-piperidine]-5-amine × 1 SO4 SULFATE ION × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M HEPES pH 7.5, 0.2 M ammonium sulphate, 28 % w/v PEG3350
Resolution 2.02 Å R-free 0.246
9BLG Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with PF-07284892 Deposited 2024-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–525（525 aa） Fragment：residues 1-525
Not recorded A1AQ1 (1S)-1'-{6-[(2-amino-3-chloropyridin-4-yl)sulfanyl]-1,2,4-triazin-3-yl}-1,3-dihydrospiro[indene-2,4'-piperidin]-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；9%PEG3350, 0.1M Bicine, pH9.2, 30mM Ammonium Acetate, 5% Tacsimate
Resolution 2.06 Å R-free 0.238
9BLG Crystal structure of non-receptor protein tyrosine phosphatase SHP2 in complex with PF-07284892 Deposited 2024-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–525（525 aa） Fragment：residues 1-525
Not recorded A1AQ1 (1S)-1'-{6-[(2-amino-3-chloropyridin-4-yl)sulfanyl]-1,2,4-triazin-3-yl}-1,3-dihydrospiro[indene-2,4'-piperidin]-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9.2；293 K；9%PEG3350, 0.1M Bicine, pH9.2, 30mM Ammonium Acetate, 5% Tacsimate
Resolution 2.06 Å R-free 0.238
9EH9 Crystal structure of unbound N-SH2 domain of SHP2 Deposited 2024-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Not recorded ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP; 500 nL of 1.0 M sodium malonate pH 5.0, 0.1 M sodium acetate trihydrate pH 4.5, and 2% w/v polyethylene glycol 20,000
Resolution 1.83 Å R-free 0.255
9EHA Crystal structure of N-SH2 domain of SHP2 bound to phosphotyrosine Deposited 2024-11-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Not recorded PTR O-PHOSPHOTYROSINE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；10 mg/mL WT N-SH2 with 20 mM O-phospho-L-tyrosine in 0.5 M Tris pH 9.0, 100 mM sodium acetate pH 4.6, and 2 M ammonium sulfate
Resolution 1.71 Å R-free 0.246
9EHD Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD Deposited 2024-11-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP, with GAB1 (QVEpYLDLDLD) 1:1.05 molar ratio; 500 nL of 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, and 25% w/v polyethylene glycol 4,000
Resolution 1.59 Å R-free 0.240
9EIC Crystal structure of unbound N-SH2 domain of SHP2 with T42A mutation Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Mutation：T42A PO4 PHOSPHATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP with 500 nL of 0.1 M Tris hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic
Resolution 1.58 Å R-free 0.218
9EIK Crystal structure of N-SH2 domain of SHP2 with T42A mutation bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD Deposited 2024-11-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Mutation：T42A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL 10 mg/mL SHP2 N-SH2 with GAB1 peptide QVEpYLDLDLD (1:1.05 molar ratio) with 500 nL 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 2.0 M Ammonium sulfate
Resolution 1.25 Å R-free 0.225
9MQ5 Crystal structure SHP2 tandem SH2 domains in complex with PZR doubly tyrosine phosphorylated ITIM peptide Deposited 2025-01-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–220（220 aa）
Not recorded EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% w/v Polyethylene glycol 3,350, 0.1 M Lithium Acetate, 0.1 M Bis-Tris pH 6.5
Resolution 1.70 Å R-free 0.229
9MUQ Crystal structure of unbound N-SH2 domain of SHP2 (1AYD conditions) Deposited 2025-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–106（106 aa） Fragment：N-terminal SH2 domain
Not recorded GOL GLYCEROL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；500 nL 20 mg/mL N-SH2 in 10 mM MES pH 5.5, 50 mM KCl; 500 nL 100 mM MES pH 6.0, 2.05 M ammonium sulfate
Resolution 1.80 Å R-free 0.266
9QCD Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide Deposited 2025-03-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–222（222 aa）
Not recorded No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 8.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å R-free 0.353
9R16 Structure of mutant SHP2 Deposited 2025-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–528（528 aa）
Mutation：Y62D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M BICINE pH 8.5 and 17% w/v PEG 4000
Resolution 2.63 Å R-free 0.304
9R16 Structure of mutant SHP2 Deposited 2025-04-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–528（528 aa）
Mutation：Y62D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M BICINE pH 8.5 and 17% w/v PEG 4000
Resolution 2.63 Å R-free 0.304
9TKT Mapping the SHP2 allosteric pocket with target-biased covalent fragments Deposited 2025-12-10 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–525（524 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 0.2M NaF, 0.1M Bis-Tris Propane pH 8.5
Resolution 2.35 Å R-free 0.283
9TKT Mapping the SHP2 allosteric pocket with target-biased covalent fragments Deposited 2025-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–525（524 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 A1JWN 3-[(1S)-1-azanylspiro[1,3-dihydroindene-2,4'-piperidine]-1'-yl]carbonylbenzenesulfonic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 0.2M NaF, 0.1M Bis-Tris Propane pH 8.5
Resolution 2.35 Å R-free 0.283
9Y5X Crystal structure of shorter construct of SHP2 unbound N-SH2 domain Deposited 2025-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–103（100 aa） Fragment：N-terminal SH2 domain
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1 M MES pH 6.0, 2.05 M ammonium sulfate
Resolution 1.80 Å R-free 0.250
9Z70 Crystal structure of shorter construct of SHP2 unbound N-SH2 domain (Y66 in blocking conformation) Deposited 2025-11-14 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 4–103（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.6 M Sodium citrate tribasic dihydrate pH 6.5
Resolution 1.73 Å R-free 0.233

114 other PDB entries and 188 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN11_HUMAN
Isoform Q06124-3
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–106； UniProt 1–106

GRB2-associated-binding protein 1

OrganismNot specified

UniProt Q13480

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 613–651 Non-standard monomer：Yes (specific site not provided by mmCIF) Isoform 3 of Tyrosine-protein phosphatase non-receptor type 11 × 1 （Q06124） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；5 % PEG3350, 0.2 M NaCl, 0.1 M BisTris, pH 5.5 Resolution 2.08 Å R-free 0.273

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9QA5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4QSY SHP2 SH2 domain in complex with GAB1 peptide Deposited 2014-07-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 621–633（13 aa） Fragment：phospho peptide, UNP residues 621-633
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；25% PEG3000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 2.10 Å R-free 0.229
9EHD Crystal structure of N-SH2 domain of SHP2 bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD Deposited 2024-11-22 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 624–633（10 aa） Fragment：residues 624-633 (Uniprot Isoform 1 numbering)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL of 10 mg/mL SHP2 N-SH2 in 50 mM Bis-Tris pH 6.5, 50 mM NaCl, 1 mM TCEP, with GAB1 (QVEpYLDLDLD) 1:1.05 molar ratio; 500 nL of 6% v/v Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, and 25% w/v polyethylene glycol 4,000
Resolution 1.59 Å R-free 0.240
9EIK Crystal structure of N-SH2 domain of SHP2 with T42A mutation bound to GAB1 tyrosine phosphorylated peptide (624-633) QVEpYLDLDLD Deposited 2024-11-26 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 624–633（10 aa） Fragment：residues 624-633 (Uniprot Isoform 1 numbering)
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；500 nL 10 mg/mL SHP2 N-SH2 with GAB1 peptide QVEpYLDLDLD (1:1.05 molar ratio) with 500 nL 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 2.0 M Ammonium sulfate
Resolution 1.25 Å R-free 0.225
9QCD Micro-ED structure of the NSH2-CSH2 tandem domain of SHP2 in complex with the bis-phosphorylated pY627-pY659-Gab1 (613-694) peptide Deposited 2025-03-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 617–683（67 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer pH 8.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å R-free 0.353

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–39； UniProt 613–651

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9qa5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qa5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qa5
Deposition date deposition_date2025-02-27
Structure title titleStructure of the N-SH2 domain of SHP2 in complex with the phosphoY627-Gab1 (613-651) peptide
Keywords keywordsSH2-domain, phosphatase, PTPN11, phospho-tyrosine, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.40 Å
Radius of gyration Rg (electron density) rg_electron12.80 Å
Forward intensity I(0) i03166530.00
Molecular weight molecular_weight12322.0 kDa
Excluded volume excluded_volume15372 ų
Envelope volume envelope_volume16895 ų
Hydration-shell volume shell_volume11178 ų
Envelope diameter envelope_diameter43.5 Å
Shell Rg shell_rg18.59 Å
Envelope Rg envelope_rg13.07 Å
Shape Rg shape_rg12.78 Å
Total Rg total_rg14.13 Å
Total atoms total_atoms870
Residues n_residues107
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax44.7 Å
Rg (real space) rg_real14.28 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real3.1670e+06
I(0) uncertainty (real space) i0_real_error3.1840e+04
Rg (reciprocal space) rg_reciprocal14.29 Å
I(0) (reciprocal space) i0_reciprocal3167000.0000
Solution quality estimate total_estimate0.8907
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.1 Å
Skewness Skewness skewness0.020
Kurtosis Kurtosis kurtosis-0.410
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha555600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)