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- PDB-9pun: HRAS complex with UM0148697 compound -

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Basic information

Entry
Database: PDB / ID: 9pun
TitleHRAS complex with UM0148697 compound
Components
  • GTPase HRas
  • UM0148697
KeywordsHYDROLASE/INHIBITOR / GTPase / Inhibitor / Macrocycle / SIGNALING PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


GTPase complex / phospholipase C activator activity / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of ruffle assembly / defense response to protozoan / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / adipose tissue development ...GTPase complex / phospholipase C activator activity / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of ruffle assembly / defense response to protozoan / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / adipose tissue development / 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 / 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 / Signaling by FGFR2 in disease / myelination / 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 / positive regulation of epithelial cell proliferation / GRB2 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / small monomeric GTPase / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / 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 / positive regulation of fibroblast proliferation / cellular senescence / chemotaxis / endocytosis / positive regulation of type II interferon production / 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 / GDP binding / DAP12 signaling / MAPK cascade / T cell receptor signaling pathway / regulation of cell population proliferation / neuron apoptotic process / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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: 2.4 Å
AuthorsJo, C. / Lavoie, H. / Therrien, M.
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 31, 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
B: GTPase HRas
C: GTPase HRas
E: UM0148697
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,96311
Polymers58,5364
Non-polymers1,4277
Water1,31573
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4713
Polymers19,0031
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4954
Polymers19,0031
Non-polymers4923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase HRas
E: UM0148697
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9974
Polymers20,5292
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.080, 83.520, 91.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 19003.320 Da / Num. of mol.: 3
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 UM0148697


Mass: 1525.832 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.: 3 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 0.1 M Tris, 0.2 M MgCl2, 26 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→45.69 Å / Num. obs: 19723 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0506 / Rpim(I) all: 0.0218 / Rrim(I) all: 0.05523 / Net I/σ(I): 24.26
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.2595 / Mean I/σ(I) obs: 8.26 / Num. unique obs: 1916 / CC1/2: 0.983 / CC star: 0.996 / Rpim(I) all: 0.1122 / Rrim(I) all: 0.2834 / % possible all: 97.16

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.95model building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.69 Å / SU ML: 0.3013 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.789
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2597 987 5.01 %
Rwork0.2077 18733 -
obs0.2103 19720 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.01 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3684 0 198 73 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323944
X-RAY DIFFRACTIONf_angle_d0.69785344
X-RAY DIFFRACTIONf_chiral_restr0.0443600
X-RAY DIFFRACTIONf_plane_restr0.0039679
X-RAY DIFFRACTIONf_dihedral_angle_d11.1369605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.35531370.31052592X-RAY DIFFRACTION97.19
2.53-2.680.33981370.25942614X-RAY DIFFRACTION97.55
2.68-2.890.29581390.24942631X-RAY DIFFRACTION97.98
2.89-3.180.27041400.22442651X-RAY DIFFRACTION98.21
3.18-3.640.29081410.20982688X-RAY DIFFRACTION98.74
3.64-4.590.22811430.17112717X-RAY DIFFRACTION99
4.59-45.690.21311500.18532840X-RAY DIFFRACTION98.81
Refinement TLS params.Method: refined / Origin x: 27.5447792454 Å / Origin y: -1.75513262944 Å / Origin z: -7.47017380957 Å
111213212223313233
T0.286626476972 Å2-0.0192026861005 Å2-0.016141700677 Å2-0.298475794789 Å20.0376870109079 Å2--0.295497867822 Å2
L0.852283226125 °2-0.111309599182 °20.0879366997754 °2-0.0888783035069 °2-0.00913002309401 °2--0.876841816934 °2
S0.0884375442092 Å °-0.0036563263589 Å °-0.0199832823025 Å °0.0163275319805 Å °-0.0564811883041 Å °-0.082124915292 Å °-0.0869426995879 Å °-0.0779113533123 Å °-0.0237019915622 Å °
Refinement TLS groupSelection details: all

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