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- PDB-9pve: HRAS complex with UM0152533 compound -

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Basic information

Entry
Database: PDB / ID: 9pve
TitleHRAS complex with UM0152533 compound
Components
  • GTPase HRas
  • UM0152533
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 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
DepositionAug 1, 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
D: GTPase HRas
I: UM0152533
J: UM0152533
K: UM0152533
L: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,93312
Polymers82,1618
Non-polymers1,7734
Water6,449358
1
A: GTPase HRas
I: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9833
Polymers20,5402
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area9040 Å2
MethodPISA
2
B: GTPase HRas
J: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9833
Polymers20,5402
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-14 kcal/mol
Surface area8160 Å2
MethodPISA
3
C: GTPase HRas
K: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9833
Polymers20,5402
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area8900 Å2
MethodPISA
4
D: GTPase HRas
L: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9833
Polymers20,5402
Non-polymers4431
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-12 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.970, 36.850, 142.030
Angle α, β, γ (deg.)90.000, 93.030, 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: 18989.295 Da / Num. of mol.: 4
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
UM0152533


Mass: 1550.842 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.3 / Details: 0.1 M Sodium citrate, 16 % 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: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→47.28 Å / Num. obs: 44960 / % possible obs: 99.49 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.78 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.106 / Net I/σ(I): 10.4
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.26 / Num. unique obs: 4441 / CC1/2: 0.696 / Rrim(I) all: 0.776 / % possible all: 99.64

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.28 Å / SU ML: 0.2542 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8255
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2425 2249 5 %
Rwork0.2016 42704 -
obs0.2036 44953 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.26 Å2
Refinement stepCycle: LAST / Resolution: 2→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 448 358 6050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315802
X-RAY DIFFRACTIONf_angle_d0.87237863
X-RAY DIFFRACTIONf_chiral_restr0.0441844
X-RAY DIFFRACTIONf_plane_restr0.0043985
X-RAY DIFFRACTIONf_dihedral_angle_d21.4546842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.32261390.30262622X-RAY DIFFRACTION99.5
2.04-2.090.33621370.28612612X-RAY DIFFRACTION99.67
2.09-2.140.30651400.2722654X-RAY DIFFRACTION99.11
2.14-2.20.28861400.24592661X-RAY DIFFRACTION99.82
2.2-2.270.27251380.23282625X-RAY DIFFRACTION99.71
2.27-2.340.27471400.22292660X-RAY DIFFRACTION99.72
2.34-2.420.27511390.22792646X-RAY DIFFRACTION99.43
2.42-2.520.25551390.22332647X-RAY DIFFRACTION99.71
2.52-2.630.26021430.21072705X-RAY DIFFRACTION99.65
2.63-2.770.27111390.20932642X-RAY DIFFRACTION99.64
2.77-2.950.24491400.19932654X-RAY DIFFRACTION99.79
2.95-3.170.24641400.20612675X-RAY DIFFRACTION99.47
3.17-3.490.24441420.17942689X-RAY DIFFRACTION99.3
3.49-40.20231420.17172704X-RAY DIFFRACTION99.61
4-5.040.18311420.15712695X-RAY DIFFRACTION99.13
5.04-47.280.23781490.20632813X-RAY DIFFRACTION98.77
Refinement TLS params.Method: refined / Origin x: 30.8975668372 Å / Origin y: 9.22946832817 Å / Origin z: 36.4835883438 Å
111213212223313233
T0.208028909322 Å2-0.0142999106953 Å2-0.00169090796929 Å2-0.166580389718 Å2-0.0243770885997 Å2--0.20685822083 Å2
L0.261596838058 °2-0.0458552468579 °2-0.0113922263493 °2--0.0186919140479 °2-0.09061816364 °2--0.155917556286 °2
S-0.0109665613778 Å °0.0415909290465 Å °-0.00326875921023 Å °-0.0162723195856 Å °0.0182685743148 Å °-0.011827544576 Å °0.000497128227105 Å °-0.000998424207007 Å °-0.00688107854942 Å °
Refinement TLS groupSelection details: all

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