+Open data
-Basic information
Entry | Database: PDB / ID: 8b6i | ||||||
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Title | KRasG12C ligand complex | ||||||
Components | GTPase KRas | ||||||
Keywords | SIGNALING PROTEIN / INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / positive regulation of glial cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / GRB2 events in EGFR signaling / EGFR Transactivation by Gastrin / SHC1 events in EGFR signaling / Signalling to RAS / GRB2 events in ERBB2 signaling / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC1 events in ERBB2 signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / protein-membrane adaptor activity / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by ERBB2 TMD/JMD mutants / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / FCERI mediated MAPK activation / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / Signaling by CSF1 (M-CSF) in myeloid cells / 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 / GDP binding / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Ca2+ pathway / RAF/MAP kinase cascade / gene expression / actin cytoskeleton organization / Ras protein signal transduction / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Phillips, C. / Breed, J. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2023 Title: Discovery of AZD4747, a Potent and Selective Inhibitor of Mutant GTPase KRAS G12C with Demonstrable CNS Penetration. Authors: Kettle, J.G. / Bagal, S.K. / Barratt, D. / Bodnarchuk, M.S. / Boyd, S. / Braybrooke, E. / Breed, J. / Cassar, D.J. / Cosulich, S. / Davies, M. / Davies, N.L. / Deng, C. / Eatherton, A. / ...Authors: Kettle, J.G. / Bagal, S.K. / Barratt, D. / Bodnarchuk, M.S. / Boyd, S. / Braybrooke, E. / Breed, J. / Cassar, D.J. / Cosulich, S. / Davies, M. / Davies, N.L. / Deng, C. / Eatherton, A. / Evans, L. / Feron, L.J. / Fillery, S. / Gleave, E.S. / Goldberg, F.W. / Cortes Gonzalez, M.A. / Guerot, C. / Haider, A. / Harlfinger, S. / Howells, R. / Jackson, A. / Johnstrom, P. / Kemmitt, P.D. / Koers, A. / Kondrashov, M. / Lamont, G.M. / Lamont, S. / Lewis, H.J. / Liu, L. / Mylrea, M. / Nash, S. / Niedbala, M.J. / Peter, A. / Phillips, C. / Pike, K. / Raubo, P. / Robb, G.R. / Ross, S. / Sanders, M.G. / Schou, M. / Simpson, I. / Steward, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b6i.cif.gz | 91.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b6i.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 8b6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b6i_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8b6i_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8b6i_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 8b6i_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/8b6i ftp://data.pdbj.org/pub/pdb/validation_reports/b6/8b6i | HTTPS FTP |
-Related structure data
Related structure data | 8b78C 7o83S S: Starting model for refinement 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: 19352.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: 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: 2.15 Å3/Da / Density % sol: 42.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 LITHIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98005 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.86 Å / Num. obs: 32694 / % possible obs: 91.8 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.037 / Rrim(I) all: 0.052 / Net I/σ(I): 11.4 / Num. measured all: 60290 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2.2 / Num. measured all: 4003 / Num. unique obs: 2162 / CC1/2: 0.924 / Rpim(I) all: 0.265 / Rrim(I) all: 0.375 / Net I/σ(I) obs: 2.2 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7o83 Resolution: 1.7→21.73 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.63 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 74.42 Å2 / Biso mean: 21.228 Å2 / Biso min: 7.2 Å2
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Refinement step | Cycle: final / Resolution: 1.7→21.73 Å
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LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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