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- PDB-9puz: HRAS complex with UM0153030 compound -

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Basic information

Entry
Database: PDB / ID: 9puz
TitleHRAS complex with UM0153030 compound
Components
  • GTPase HRas
  • UM0153030
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 / PHOSPHATE ION / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: UM0153030
F: UM0153030
G: UM0153030
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,33116
Polymers61,5486
Non-polymers1,78210
Water2,558142
1
A: GTPase HRas
E: UM0153030
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1746
Polymers20,5162
Non-polymers6574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-31 kcal/mol
Surface area8560 Å2
MethodPISA
2
B: GTPase HRas
F: UM0153030
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0795
Polymers20,5162
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-33 kcal/mol
Surface area8550 Å2
MethodPISA
3
C: GTPase HRas
G: UM0153030
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0795
Polymers20,5162
Non-polymers5623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-28 kcal/mol
Surface area8480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.720, 85.720, 136.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

21C-545-

HOH

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCEFG

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


Mass: 18875.191 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 UM0153030


Mass: 1640.965 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 152 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: 0.1 M Tris, 0.2 M CaCl2, 22 % PEG 4,000

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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: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→37.12 Å / Num. obs: 38269 / % possible obs: 99.61 % / Redundancy: 10.1 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05776 / Rpim(I) all: 0.01934 / Rrim(I) all: 0.06097 / Net I/σ(I): 20.79
Reflection shellResolution: 2→2.071 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.001 / Mean I/σ(I) obs: 2.65 / Num. unique obs: 3713 / CC1/2: 0.861 / CC star: 0.962 / Rpim(I) all: 0.3346 / Rrim(I) all: 1.056 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.12 Å / SU ML: 0.2686 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.1498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 1901 4.99 %
Rwork0.2094 36230 -
obs0.2117 38131 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.96 Å2
Refinement stepCycle: LAST / Resolution: 2→37.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 380 142 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374542
X-RAY DIFFRACTIONf_angle_d0.78426175
X-RAY DIFFRACTIONf_chiral_restr0.0446661
X-RAY DIFFRACTIONf_plane_restr0.0043786
X-RAY DIFFRACTIONf_dihedral_angle_d13.6148779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.34591370.31112593X-RAY DIFFRACTION99.85
2.05-2.110.32981350.27422571X-RAY DIFFRACTION99.89
2.11-2.170.31360.262590X-RAY DIFFRACTION100
2.17-2.240.27481340.24062595X-RAY DIFFRACTION99.74
2.24-2.320.29361370.23352594X-RAY DIFFRACTION99.78
2.32-2.410.29241350.23242566X-RAY DIFFRACTION99.67
2.41-2.520.30971360.23952603X-RAY DIFFRACTION99.38
2.52-2.650.28461330.23612551X-RAY DIFFRACTION99.78
2.65-2.820.35361370.23622589X-RAY DIFFRACTION99.74
2.82-3.040.25431360.22022601X-RAY DIFFRACTION99.71
3.04-3.340.23661350.22392585X-RAY DIFFRACTION99.85
3.34-3.820.22961370.18882599X-RAY DIFFRACTION99.89
3.83-4.820.20921360.16842601X-RAY DIFFRACTION99.67
4.82-37.120.23721370.19432592X-RAY DIFFRACTION98.09
Refinement TLS params.Method: refined / Origin x: -38.8542380005 Å / Origin y: -2.33288596989 Å / Origin z: 7.38743726614 Å
111213212223313233
T0.332799312467 Å2-0.0465743485736 Å20.0113025580893 Å2-0.252349247266 Å2-0.0140816948836 Å2--0.377029686111 Å2
L0.0782601529514 °2-0.17625782865 °20.112115758525 °2-0.0519427670856 °2-0.109632758871 °2--0.745717977905 °2
S0.0232053446154 Å °-0.0166677901312 Å °-0.0249996222884 Å °0.00412019766955 Å °0.0527072077726 Å °-0.0135088527028 Å °-0.00747674110907 Å °0.0026721894667 Å °-0.0735042539739 Å °
Refinement TLS groupSelection details: all

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