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- PDB-9pu3: HRAS complex with UM0140692 compound -

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Basic information

Entry
Database: PDB / ID: 9pu3
TitleHRAS complex with UM0140692 compound
Components
  • GTPase HRas
  • UM0140692
KeywordsHYDROLASE/INHIBITOR / GTPase / Inhibitor / Macrocycle / SIGNALING PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of ruffle assembly / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of ruffle assembly / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / adipose tissue development / SOS-mediated signalling / positive regulation of protein targeting to membrane / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Schwann cell development / 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 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / protein-membrane adaptor activity / myelination / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / Downstream signal transduction / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of epithelial cell proliferation / animal organ morphogenesis / VEGFR2 mediated cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / RAF activation / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / cellular response to gamma radiation / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / chemotaxis / endocytosis / cellular senescence / 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 / Negative regulation of MAPK pathway / RAS processing / Regulation of RAS by GAPs / insulin receptor signaling pathway / Signaling by BRAF and RAF1 fusions / DAP12 signaling / GDP binding / MAPK cascade / regulation of cell population proliferation / T cell receptor signaling pathway / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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
GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJo, C. / Lavoie, H. / Therrien, M. / Arya, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2026
Title: Targeting the H/KRAS alpha 4-beta 6-alpha 5 Allosteric Lobe with Macrocyclic Peptides.
Authors: Tran, K. / Lavoie, H. / Wahhab, A. / Garrido, D. / Jo, C.H. / Poupart, M.A. / Arya, T. / Beautrait, A. / Killoran, R. / Dicaire-Leduc, C. / Bonneil, E. / Osborne, M. / Schuetz, D.A. / ...Authors: Tran, K. / Lavoie, H. / Wahhab, A. / Garrido, D. / Jo, C.H. / Poupart, M.A. / Arya, T. / Beautrait, A. / Killoran, R. / Dicaire-Leduc, C. / Bonneil, E. / Osborne, M. / Schuetz, D.A. / Shaikh, F. / Thibault, P. / Smith, M.J. / Marinier, A. / Therrien, M.
History
DepositionJul 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
C: UM0140692
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7924
Polymers20,3252
Non-polymers4682
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-24 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.754, 37.232, 63.070
Angle α, β, γ (deg.)90.000, 91.220, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18875.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01112, small monomeric GTPase
#2: Protein/peptide UM0140692


Mass: 1449.738 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GDP / GUANOSINE-5'-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.84 Å3/Da / Density % sol: 33.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.7→63.06 Å / Num. obs: 15867 / % possible obs: 96.09 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.07 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06533 / Rrim(I) all: 0.07851 / Net I/σ(I): 15.96
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 6.63 % / Rmerge(I) obs: 0.1514 / Mean I/σ(I) obs: 6.63 / Num. unique obs: 1502 / CC1/2: 0.978 / CC star: 0.994 / Rrim(I) all: 0.1834 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→63.06 Å / SU ML: 0.1886 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 22.8268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 1592 10.05 %
Rwork0.1708 14248 -
obs0.1754 15840 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.52 Å2
Refinement stepCycle: LAST / Resolution: 1.7→63.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 133 230 1671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00491507
X-RAY DIFFRACTIONf_angle_d0.96432054
X-RAY DIFFRACTIONf_chiral_restr0.0545224
X-RAY DIFFRACTIONf_plane_restr0.0066265
X-RAY DIFFRACTIONf_dihedral_angle_d9.7194253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.31731340.24731239X-RAY DIFFRACTION91.05
1.76-1.820.28431420.22311228X-RAY DIFFRACTION94.42
1.82-1.890.25471420.19171286X-RAY DIFFRACTION95.2
1.89-1.980.21341520.17561267X-RAY DIFFRACTION96.01
1.98-2.080.22951370.17771289X-RAY DIFFRACTION95.51
2.08-2.210.22041530.17411259X-RAY DIFFRACTION94.01
2.21-2.380.19721520.17421288X-RAY DIFFRACTION97.04
2.38-2.620.22941530.16171322X-RAY DIFFRACTION98.2
2.62-30.23491400.16771322X-RAY DIFFRACTION97.79
3-3.780.16021350.15261367X-RAY DIFFRACTION98.04
3.78-63.060.20941520.15651381X-RAY DIFFRACTION98.52

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