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- PDB-8jjs: Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhib... -

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Basic information

Entry
Database: PDB / ID: 8jjs
TitleHuman K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP10343
Components
  • Isoform 2B of GTPase KRas
  • MAA-ILE-SAR-SAR-7T2-SAR-IAE-LEU-MEA-MLE-7TK
KeywordsSIGNALING PROTEIN/INHIBITOR / CYCLIC PEPTIDE / ONCOLOGY / SIGNALING PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / 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 / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / 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 / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / 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 / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / 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 / GDP binding / 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 / 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 / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.534 Å
AuthorsIrie, M. / Fukami, T.A. / Tanada, M. / Ohta, A. / Torizawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Am.Chem.Soc. / Year: 2023
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
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
I: MAA-ILE-SAR-SAR-7T2-SAR-IAE-LEU-MEA-MLE-7TK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3307
Polymers21,5752
Non-polymers7565
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-68 kcal/mol
Surface area8590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.596, 66.596, 86.613
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AI

#1: Protein Isoform 2B of GTPase KRas


Mass: 20150.582 Da / Num. of mol.: 1 / Mutation: G12D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLacI / References: UniProt: P01116
#2: Protein/peptide MAA-ILE-SAR-SAR-7T2-SAR-IAE-LEU-MEA-MLE-7TK


Mass: 1424.091 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 127 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.0 M Ammonium sulfate, 25 %(v/v) Ethylene glycol as cryoprotectant

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.045 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 1.534→57.674 Å / Num. obs: 21593 / % possible obs: 95 % / Redundancy: 20.49 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.329 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.0232 / Rrim(I) all: 0.1065 / AbsDiff over sigma anomalous: 0.743 / Baniso tensor eigenvalue 1: 30.8 Å2 / Baniso tensor eigenvalue 2: 30.8 Å2 / Baniso tensor eigenvalue 3: 17.8 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.856 Å / Aniso diffraction limit 2: 1.856 Å / Aniso diffraction limit 3: 1.499 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 19.1 / Num. measured all: 442425 / Orthogonalization convention: pdb / % possible anomalous: 94.4 / % possible ellipsoidal: 95 / % possible ellipsoidal anomalous: 94.4 / % possible spherical: 66.2 / % possible spherical anomalous: 65.8 / Redundancy anomalous: 10.42
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.808-57.67420.950.035871.522262422624108010800.999-0.5670.0080.03670.81899.599.999.599.999.510.9899.9
3.819-4.80821.990.039568.842379623796108210820.999-0.4490.00860.04040.7510010010010010011.28100
3.326-3.81922.230.053155.192389323893107510750.999-0.3540.01150.05430.78410010010010010011.32100
3.02-3.32622.380.075339.692412324123107810780.999-0.3070.01620.0770.77310010010010010011.42100
2.801-3.0222.30.107329.982417524175108410840.997-0.2090.02330.10990.78610010010010010011.32100
2.638-2.80119.340.140620.452087320873107910790.996-0.1130.03270.14440.7811001001001001009.88100
2.504-2.63817.850.169616.621930119301108110810.994-0.1150.04120.17460.7761001001001001009.1100
2.393-2.50419.140.214414.312061820618107710770.993-0.0150.05030.22030.7771001001001001009.71100
2.301-2.39320.210.253312.52186321863108210820.994-0.0410.05770.25980.74710010010010010010.22100
2.22-2.30120.740.337110.172235522355107810780.987-0.0550.07570.34560.76410010010010010010.48100
2.151-2.2221.030.39938.712277622776108310830.986-0.0830.08890.40910.7110010010010010010.63100
2.088-2.15121.190.49137.222283922839107810780.9790.0210.10880.50330.75410010010010010010.71100
2.035-2.08821.270.63975.622290822908107710770.9740.0080.14110.65520.74699.910099.910099.910.76100
1.984-2.03521.480.80724.512323823238108210820.95-0.0360.17710.82650.7110010010010010010.86100
1.94-1.98421.520.96573.812320123201107810780.94-0.0630.21150.98870.71410010010010010010.88100
1.897-1.9421.651.22563.032335923359107910790.902-0.0780.26731.25460.68399.899.799.899.799.810.9299.7
1.855-1.89721.571.37912.692335823358108310830.895-0.0040.30081.41170.6929190.29190.29110.8590.2
1.787-1.85520.271.18423.052190921909108110810.894-0.0850.26631.2140.72472.372.472.349.350.310.1572.4
1.694-1.78718.881.34482.482025520255107310730.829-0.0590.31251.38110.67973.773.973.73030.59.4673.9
1.534-1.69413.811.53591.741496114961108310830.671-0.0240.41511.59310.70473.881.973.812.911.97.4181.9

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Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
XDSJan 31, 2020data reduction
Aimless0.7.7data scaling
pointless1.12.12data scaling
STARANISO2.3.63data scaling
BUSTER2.11.8refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.534→57.67 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.116 / SU Rfree Cruickshank DPI: 0.116
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 1056 4.89 %RANDOM
Rwork0.2207 ---
obs0.2217 21593 66.3 %-
Displacement parametersBiso max: 77.55 Å2 / Biso mean: 27.04 Å2 / Biso min: 10.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.3308 Å20 Å20 Å2
2--0.3308 Å20 Å2
3----0.6617 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.534→57.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 44 122 1609
Biso mean--36.99 35.82 -
Num. residues----180
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d559SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes260HARMONIC5
X-RAY DIFFRACTIONt_it1510HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion195SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1440SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1510HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg2054HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion15.33
LS refinement shellResolution: 1.534→1.62 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2334 21 4.86 %
Rwork0.277 411 -
obs--8.52 %

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