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Yorodumi- PDB-8t7q: Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t7q | ||||||
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Title | Identification of GDC-1971 (RLY-1971), a SHP2 inhibitor designed for the treatment of solid tumors | ||||||
Components | Tyrosine-protein phosphatase non-receptor type 11 | ||||||
Keywords | HYDROLASE / Phosphatase / Tumor target / inhibitor | ||||||
Function / homology | Function and homology information negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion ...negative regulation of cortisol secretion / intestinal epithelial cell migration / microvillus organization / negative regulation of growth hormone secretion / genitalia development / atrioventricular canal development / negative regulation of cell adhesion mediated by integrin / STAT5 Activation / Netrin mediated repulsion signals / positive regulation of hormone secretion / cerebellar cortex formation / multicellular organismal reproductive process / regulation of protein export from nucleus / positive regulation of ossification / hormone metabolic process / Interleukin-37 signaling / Signaling by Leptin / negative regulation of chondrocyte differentiation / MET activates PTPN11 / Regulation of RUNX1 Expression and Activity / face morphogenesis / ERBB signaling pathway / Costimulation by the CD28 family / Signal regulatory protein family interactions / peptide hormone receptor binding / negative regulation of type I interferon production / platelet formation / megakaryocyte development / organ growth / CTLA4 inhibitory signaling / triglyceride metabolic process / Platelet sensitization by LDL / Interleukin-20 family signaling / PI-3K cascade:FGFR3 / Interleukin-6 signaling / STAT5 activation downstream of FLT3 ITD mutants / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / Prolactin receptor signaling / PI-3K cascade:FGFR1 / MAPK3 (ERK1) activation / PECAM1 interactions / MAPK1 (ERK2) activation / regulation of cell adhesion mediated by integrin / regulation of type I interferon-mediated signaling pathway / Bergmann glial cell differentiation / phosphoprotein phosphatase activity / inner ear development / neurotrophin TRK receptor signaling pathway / platelet-derived growth factor receptor signaling pathway / non-membrane spanning protein tyrosine phosphatase activity / RET signaling / peptidyl-tyrosine dephosphorylation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of IFNA/IFNB signaling / PI3K Cascade / PD-1 signaling / regulation of protein-containing complex assembly / ephrin receptor signaling pathway / fibroblast growth factor receptor signaling pathway / GAB1 signalosome / Activated NTRK2 signals through FRS2 and FRS3 / negative regulation of insulin secretion / Regulation of IFNG signaling / positive regulation of insulin receptor signaling pathway / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Tie2 Signaling / FRS-mediated FGFR1 signaling / cellular response to epidermal growth factor stimulus / cell adhesion molecule binding / GPVI-mediated activation cascade / T cell costimulation / FLT3 Signaling / positive regulation of interferon-beta production / hormone-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of mitotic cell cycle / Downstream signal transduction / protein dephosphorylation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine kinase binding / DNA damage checkpoint signaling / protein tyrosine phosphatase activity / integrin-mediated signaling pathway / positive regulation of glucose import / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Spry regulation of FGF signaling / insulin receptor binding / epidermal growth factor receptor signaling pathway / multicellular organism growth Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Tang, Y. / Nguyen, V. / Wilbur, J.D. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors. Authors: Taylor, A.M. / Williams, B.R. / Giordanetto, F. / Kelley, E.H. / Lescarbeau, A. / Shortsleeves, K. / Tang, Y. / Walters, W.P. / Arrazate, A. / Bowman, C. / Brophy, E. / Chan, E.W. / ...Authors: Taylor, A.M. / Williams, B.R. / Giordanetto, F. / Kelley, E.H. / Lescarbeau, A. / Shortsleeves, K. / Tang, Y. / Walters, W.P. / Arrazate, A. / Bowman, C. / Brophy, E. / Chan, E.W. / Deshmukh, G. / Greisman, J.B. / Hunsaker, T.L. / Kipp, D.R. / Saenz Lopez-Larrocha, P. / Maddalo, D. / Martin, I.J. / Maragakis, P. / Merchant, M. / Murcko, M. / Nisonoff, H. / Nguyen, V. / Nguyen, V. / Orozco, O. / Owen, C. / Pierce, L. / Schmidt, M. / Shaw, D.E. / Smith, S. / Therrien, E. / Tran, J.C. / Watters, J. / Waters, N.J. / Wilbur, J. / Willmore, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t7q.cif.gz | 266.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t7q.ent.gz | 171.2 KB | Display | PDB format |
PDBx/mmJSON format | 8t7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t7q_validation.pdf.gz | 371.1 KB | Display | wwPDB validaton report |
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Full document | 8t7q_full_validation.pdf.gz | 372.8 KB | Display | |
Data in XML | 8t7q_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 8t7q_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/8t7q ftp://data.pdbj.org/pub/pdb/validation_reports/t7/8t7q | HTTPS FTP |
-Related structure data
Related structure data | 8t6dC 8t6gC 8t8qC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 60335.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN11, PTP2C, SHPTP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06124, protein-tyrosine-phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 19% PEG 3350,100 mM Tris-HCl (pH 8.5), 300 mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 101 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.4 Å / Num. obs: 56960 / % possible obs: 92.2 % / Redundancy: 2 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0547 / Net I/σ(I): 8.45 |
Reflection shell | Resolution: 2.1→2.18 Å / Num. unique obs: 6154 / CC1/2: 0.837 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→55.4 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.0425 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→55.4 Å
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Refine LS restraints |
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LS refinement shell |
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