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- PDB-7yv1: Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yv1 | |||||||||
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Title | Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor LUNA18 and KA30L Fab | |||||||||
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![]() | SIGNALING PROTEIN / K-RAS / CYCLIC PEPTIDE / ONCOLOGY / SIGNALING PROTEIN-INHIBITOR COMPLEX | |||||||||
Function / homology | ![]() forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / 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 / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / 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 / 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 / Signalling to RAS / SHC-related events triggered by IGF1R / glial cell proliferation / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / 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 / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / mitochondrial outer membrane / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Irie, M. / Fukami, T.A. / Matsuo, A. / Saka, K. / Nishimura, M. / Saito, H. / Torizawa, T. / Tanada, M. / Ohta, A. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Validation of a New Methodology to Create Oral Drugs beyond the Rule of 5 for Intracellular Tough Targets. Authors: Ohta, A. / Tanada, M. / Shinohara, S. / Morita, Y. / Nakano, K. / Yamagishi, Y. / Takano, R. / Kariyuki, S. / Iida, T. / Matsuo, A. / Ozeki, K. / Emura, T. / Sakurai, Y. / Takano, K. / ...Authors: Ohta, A. / Tanada, M. / Shinohara, S. / Morita, Y. / Nakano, K. / Yamagishi, Y. / Takano, R. / Kariyuki, S. / Iida, T. / Matsuo, A. / Ozeki, K. / Emura, T. / Sakurai, Y. / Takano, K. / Higashida, A. / Kojima, M. / Muraoka, T. / Takeyama, R. / Kato, T. / Kimura, K. / Ogawa, K. / Ohara, K. / Tanaka, S. / Kikuchi, Y. / Hisada, N. / Hayashi, R. / Nishimura, Y. / Nomura, K. / Tachibana, T. / Irie, M. / Kawada, H. / Torizawa, T. / Murao, N. / Kotake, T. / Tanaka, M. / Ishikawa, S. / Miyake, T. / Tamiya, M. / Arai, M. / Chiyoda, A. / Akai, S. / Sase, H. / Kuramoto, S. / Ito, T. / Shiraishi, T. / Kojima, T. / Iikura, H. #1: ![]() Title: Development of Orally Bioavailable Peptides Targeting an Intracellular Protein: From a Hit to a Clinical KRAS Inhibitor Authors: Tanada, M. / Tamiya, M. / Matsuo, A. / Chiyoda, A. / Takano, K. / Ito, T. / Irie, M. / Kotake, T. / Takeyama, R. / Kawada, H. / Hayashi, R. / Ishikawa, S. / Nomura, K. / Furuichi, N. / ...Authors: Tanada, M. / Tamiya, M. / Matsuo, A. / Chiyoda, A. / Takano, K. / Ito, T. / Irie, M. / Kotake, T. / Takeyama, R. / Kawada, H. / Hayashi, R. / Ishikawa, S. / Nomura, K. / Furuichi, N. / Morita, Y. / Kage, M. / Hashimoto, S. / Nii, K. / Sase, H. / Ohara, K. / Ohta, A. / Kuramoto, S. / Nishimura, Y. / Iikura, H. / Shiraishi, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.6 KB | Display | ![]() |
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PDB format | ![]() | 123.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.8 KB | Display | ![]() |
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Full document | ![]() | 485.8 KB | Display | |
Data in XML | ![]() | 35.5 KB | Display | |
Data in CIF | ![]() | 56.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yuzC ![]() 7vo2 S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 24116.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#3: Antibody | Mass: 23242.715 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Protein/peptide , 2 types, 2 molecules AI
#1: Protein | Mass: 20150.582 Da / Num. of mol.: 1 / Mutation: G12D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein/peptide | Mass: 1455.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 1074 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
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#5: Chemical | ChemComp-GDP / |
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#6: Chemical | ChemComp-MG / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.0 %v/v Tacsimate (pH 5.0), 0.1 M tri-Sodium citrate (pH 5.6), 16.0 %w/v Polyethylene glycol 3,350, and 25 %v/v Ethylene glycerol as a cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.454→58.41 Å / Num. obs: 97915 / % possible obs: 90.3 % / Redundancy: 9.35 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1335 / Rpim(I) all: 0.0442 / Rrim(I) all: 0.141 / Net I/σ(I): 16.42 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VO2 ![]() 7vo2 Resolution: 1.454→58.41 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.106
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Displacement parameters | Biso max: 76.89 Å2 / Biso mean: 15.17 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.454→58.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.454→1.49 Å / Rfactor Rfree error: 0
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