+
Open data
-
Basic information
Entry | Database: PDB / ID: 7yce | ||||||
---|---|---|---|---|---|---|---|
Title | KRas G12C in complex with Compound 7b | ||||||
![]() | Isoform 2B of GTPase KRas | ||||||
![]() | ONCOPROTEIN/inhibitor / ONCOPROTEIN-inhibitor complex | ||||||
Function / homology | small monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Chem-IQN / Isoform 2B of GTPase KRas![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Amano, Y. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Discovery and biological evaluation of 1-{2,7-diazaspiro[3.5]nonan-2-yl}prop-2-en-1-one derivatives as covalent inhibitors of KRAS G12C with favorable metabolic stability and anti-tumor activity. Authors: Imaizumi, T. / Akaiwa, M. / Abe, T. / Nigawara, T. / Koike, T. / Satake, Y. / Watanabe, K. / Kaneko, O. / Amano, Y. / Mori, K. / Yamanaka, Y. / Nagashima, T. / Shimazaki, M. / Kuramoto, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 55.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 14.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yccC ![]() 4l8gS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19358.836 Da / Num. of mol.: 1 / Mutation: G12C, C118S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 99 molecules ![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IQN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/IQN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GDP / |
---|---|
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-SO4 / |
#5: Chemical | ChemComp-IQN / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.89 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, ammonium sulfate, PEG550MME |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jun 9, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→22.94 Å / Num. obs: 17961 / % possible obs: 92.9 % / Redundancy: 8.7 % / CC1/2: 0.987 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.025 / Rrim(I) all: 0.073 / Net I/σ(I): 18.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4L8G Resolution: 1.8→22.94 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.872 / SU B: 4.501 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||
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: 97.79 Å2 / Biso mean: 25.494 Å2 / Biso min: 8.49 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→22.94 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|