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- PDB-8pi0: NMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 5-(1H-... -

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Basic information

Entry
Database: PDB / ID: 8pi0
TitleNMR2 Structure of KRAS G12V (GMPPNP bound) in complex with 5-(1H-indol-2-l)piperazin-2-one
ComponentsV-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
KeywordsONCOPROTEIN / Complex / Fragment
Function / homology
Function and homology information


endocrine signaling / forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / glial cell proliferation ...endocrine signaling / forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / glial cell proliferation / protein-membrane adaptor activity / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / striated muscle cell differentiation / regulation of long-term neuronal synaptic plasticity / visual learning / actin cytoskeleton organization / neuron apoptotic process / negative regulation of neuron apoptotic process / GTPase activity / positive regulation of gene expression / GTP binding / membrane
Similarity search - Function
small GTPase Rab1 family profile. / small GTPase Rho family profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / 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
: / V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBuetikofer, M. / Orts, J.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss Cancer LeagueKFS-4903-08-2019 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: NMR2-Based Drug Discovery Pipeline Presented on the Oncogenic Protein KRAS.
Authors: Butikofer, M. / Torres, F. / Kadavath, H. / Gamperli, N. / Abi Saad, M.J. / Zindel, D. / Coudevylle, N. / Riek, R. / Orts, J.
History
DepositionJun 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3842
Polymers19,1691
Non-polymers2151
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)4 / 4structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b


Mass: 19168.592 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, hCG_14731 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A024RAV5
#2: Chemical ChemComp-YVW / (5~{S})-5-(1~{H}-indol-2-yl)piperazin-2-one


Mass: 215.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N3O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H NOESY
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-13C; U-15N] KRAS, 5.0 mM 5-(1H-indol-2-yl)piperazin-2-one, 100% D2O
Label: 13C_sample, 15N_sample / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMKRAS[U-13C; U-15N]1
5.0 mM5-(1H-indol-2-yl)piperazin-2-onenatural abundance1
Sample conditionsIonic strength: 125 mM / Label: conditions_1 / pH: 7.4 pD / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE NEO / Manufacturer: Bruker / Model: AVANCE NEO / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
HADDOCKBonvinrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4 / Conformers submitted total number: 4

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