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Yorodumi- PDB-9axh: Crystal structure of KSR1/MEK1 complex heterotetramer with NST-628 -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9axh | ||||||
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| Title | Crystal structure of KSR1/MEK1 complex heterotetramer with NST-628 | ||||||
Components |
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Keywords | TRANSFERASE / Inhibitor / complex / SIGNALING PROTEIN | ||||||
| Function / homology | Function and homology informationregulation of MAP kinase activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development / MAP-kinase scaffold activity ...regulation of MAP kinase activity / epithelial cell proliferation involved in lung morphogenesis / positive regulation of endodermal cell differentiation / negative regulation of homotypic cell-cell adhesion / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / regulation of vascular associated smooth muscle contraction / mitogen-activated protein kinase kinase / Golgi inheritance / placenta blood vessel development / MAP-kinase scaffold activity / positive regulation of muscle contraction / regulation of axon regeneration / cerebellar cortex formation / labyrinthine layer development / melanosome transport / type B pancreatic cell proliferation / Signaling by MAP2K mutants / vesicle transport along microtubule / positive regulation of axonogenesis / positive regulation of Ras protein signal transduction / regulation of Golgi inheritance / mitogen-activated protein kinase kinase kinase binding / central nervous system neuron differentiation / triglyceride homeostasis / trachea formation / Negative feedback regulation of MAPK pathway / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / Frs2-mediated activation / MAPK3 (ERK1) activation / ERBB2-ERBB3 signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / face development / endodermal cell differentiation / MAP kinase kinase activity / Bergmann glial cell differentiation / positive regulation of ATP biosynthetic process / thyroid gland development / Uptake and function of anthrax toxins / positive regulation of protein serine/threonine kinase activity / protein kinase activator activity / Schwann cell development / response to axon injury / keratinocyte differentiation / neuron projection morphogenesis / 14-3-3 protein binding / ERK1 and ERK2 cascade / myelination / protein serine/threonine/tyrosine kinase activity / positive regulation of autophagy / dendrite cytoplasm / insulin-like growth factor receptor signaling pathway / response to glucocorticoid / MAP3K8 (TPL2)-dependent MAPK1/3 activation / thymus development / protein serine/threonine kinase activator activity / Signal transduction by L1 / cell motility / positive regulation of transcription elongation by RNA polymerase II / RAF activation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / small GTPase binding / ruffle membrane / neuron differentiation / chemotaxis / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / cellular senescence / Signaling by BRAF and RAF1 fusions / late endosome / MAPK cascade / regulation of cell population proliferation / heart development / response to oxidative stress / protein tyrosine kinase activity / scaffold protein binding / cell cortex / perikaryon / microtubule / Ras protein signal transduction / early endosome / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / positive regulation of MAPK cascade / postsynaptic density / positive regulation of cell migration / ciliary basal body / negative regulation of cell population proliferation / axon / negative regulation of gene expression / protein serine kinase activity / focal adhesion / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / centrosome Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | ||||||
Authors | Quade, B. / Huang, X. | ||||||
| Funding support | 1items
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Citation | Journal: Cancer Discov / Year: 2024Title: The Pan-RAF-MEK Nondegrading Molecular Glue NST-628 Is a Potent and Brain-Penetrant Inhibitor of the RAS-MAPK Pathway with Activity across Diverse RAS- and RAF-Driven Cancers. Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Ayşegül Özen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / ...Authors: Meagan B Ryan / Bradley Quade / Natasha Schenk / Zhong Fang / Marshall Zingg / Steven E Cohen / Brooke M Swalm / Chun Li / Ayşegül Özen / Chaoyang Ye / Maria Stella Ritorto / Xin Huang / Arvin C Dar / Yongxin Han / Klaus P Hoeflich / Michael Hale / Margit Hagel / ![]() Abstract: Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the ...Alterations in the RAS-MAPK signaling cascade are common across multiple solid tumor types and are a driver for many cancers. NST-628 is a potent pan-RAF-MEK molecular glue that prevents the phosphorylation and activation of MEK by RAF, overcoming the limitations of traditional RAS-MAPK inhibitors and leading to deep durable inhibition of the pathway. Cellular, biochemical, and structural analyses of RAF-MEK complexes show that NST-628 engages all isoforms of RAF and prevents the formation of BRAF-CRAF heterodimers, a differentiated mechanism from all current RAF inhibitors. With a potent and durable inhibition of the RAF-MEK signaling complex as well as high intrinsic permeability into the brain, NST-628 demonstrates broad efficacy in cellular and patient-derived tumor models harboring diverse MAPK pathway alterations, including orthotopic intracranial models. Given its functional and pharmacokinetic mechanisms that are differentiated from previous therapies, NST-628 is positioned to make an impact clinically in areas of unmet patient need. Significance: This study introduces NST-628, a molecular glue having differentiated mechanism and drug-like properties. NST-628 treatment leads to broad efficacy with high tolerability and central nervous system activity across multiple RAS- and RAF-driven tumor models. NST-628 has the potential to provide transformative clinical benefits as both monotherapy and vertical combination anchor. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9axh.cif.gz | 529.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9axh.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9axh.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9axh_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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| Full document | 9axh_full_validation.pdf.gz | 1.9 MB | Display | |
| Data in XML | 9axh_validation.xml.gz | 39.9 KB | Display | |
| Data in CIF | 9axh_validation.cif.gz | 53.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/9axh ftp://data.pdbj.org/pub/pdb/validation_reports/ax/9axh | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9axaC ![]() 9axcC ![]() 9axmC ![]() 9axxC ![]() 9axyC ![]() 9ay7C ![]() 9ayaC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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Components
-Protein , 2 types, 4 molecules ABCD
| #1: Protein | Mass: 34575.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1, MEK1, PRKMK1 / Production host: Homo sapiens (human)References: UniProt: Q02750, mitogen-activated protein kinase kinase #2: Protein | Mass: 32458.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KSR1, KSR / Production host: Homo sapiens (human)References: UniProt: Q8IVT5, non-specific serine/threonine protein kinase |
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-Non-polymers , 6 types, 23 molecules 








| #3: Chemical | Mass: 488.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H18F2N4O5S / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-ANP / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-EDO / | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
| 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: 2.33 Å3/Da / Density % sol: 47.1 % |
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| Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M SPG buffer pH 7.0, 25% w/v PEG 1500 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97629 Å |
| Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 6, 2023 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 |
| Reflection | Resolution: 2.81→52.24 Å / Num. obs: 30392 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 85.77 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18 |
| Reflection shell | Resolution: 2.81→2.91 Å / Rmerge(I) obs: 0.67 / Num. unique obs: 2553 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→52.24 Å / SU ML: 0.3919 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4532 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: 92.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.81→52.24 Å
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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Homo sapiens (human)
X-RAY DIFFRACTION
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