Tyrosine-protein phosphatase non-receptor type 11
Homo sapiens
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1–525 | Fragment：UNP residues 1-525 | 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 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1–525 | Fragment：UNP residues 1-525 | 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 |
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 5EHP | 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 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 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 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 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 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 ligand/ion 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 oligomeric state 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 oligomeric state 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：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 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 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）
|
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 |
| 5EHR Non-receptor Protein Tyrosine Phosphatase SHP2 in Complex with Allosteric Inhibitor SHP099 Deposited 2015-10-28 | 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 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 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 | 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 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 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：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 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：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 mutation/modification 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
|
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 mutation/modification 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
|
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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：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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 | 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 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）
|
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 ligand/ion 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 oligomeric state 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
|
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 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 oligomeric state 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
|
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 oligomeric state 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 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 |
| 9QA5 Structure of the N-SH2 domain of SHP2 in complex with the phosphoY627-Gab1 (613-651) peptide Deposited 2025-02-27 | Different construct Different oligomeric state 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）
|
Not recorded | No recorded non-water small molecule |
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 |
| 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 oligomeric state Different ligand/ion 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 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）
|
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 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）
|
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 ligand/ion 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 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 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 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）
|
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 187 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PTN11_HUMAN |
| Isoform | Q06124-2 |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–526； UniProt 1–525 Author chain B； PDBConstruct 2–526； UniProt 1–525 |
