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- PDB-9pul: HRAS complex with UM0143525 compound -

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Basic information

Entry
Database: PDB / ID: 9pul
TitleHRAS complex with UM0143525 compound
Components
  • GTPase HRas
  • UM0143525
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: 2.5 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
D: GTPase HRas
E: UM0143525
F: UM0143525
G: UM0143525
H: UM0143525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,12416
Polymers82,2548
Non-polymers1,8708
Water1,42379
1
A: GTPase HRas
E: UM0143525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,5642
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-24 kcal/mol
Surface area9120 Å2
MethodPISA
2
B: GTPase HRas
F: UM0143525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,5642
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-22 kcal/mol
Surface area8230 Å2
MethodPISA
3
C: GTPase HRas
G: UM0143525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,5642
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-24 kcal/mol
Surface area8720 Å2
MethodPISA
4
D: GTPase HRas
H: UM0143525
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0314
Polymers20,5642
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-22 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.780, 37.530, 143.120
Angle α, β, γ (deg.)90.000, 95.800, 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: 19017.346 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
UM0143525


Mass: 1546.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.06 Å3/Da / Density % sol: 40.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris, 0.2 M CaCl2, 18 % 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: 1.1806 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: 1.1806 Å / Relative weight: 1
ReflectionResolution: 2.36→36.31 Å / Num. obs: 23886 / % possible obs: 99.49 % / Redundancy: 6 % / Biso Wilson estimate: 11.7 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.114 / Net I/σ(I): 6.9
Reflection shellResolution: 2.36→2.55 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.53 / Num. unique obs: 2308 / CC1/2: 0.877 / Rrim(I) all: 1.126 / % possible all: 99.48

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Coot0.9.8.95model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.31 Å / SU ML: 0.4571 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.01
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2673 1195 5 %
Rwork0.2145 22685 -
obs0.2172 23880 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 472 79 5680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00275709
X-RAY DIFFRACTIONf_angle_d0.67637741
X-RAY DIFFRACTIONf_chiral_restr0.0426843
X-RAY DIFFRACTIONf_plane_restr0.0096984
X-RAY DIFFRACTIONf_dihedral_angle_d13.6191980
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.66141290.5792451X-RAY DIFFRACTION99.61
2.6-2.720.39451310.32292486X-RAY DIFFRACTION99.43
2.72-2.860.36131320.25832500X-RAY DIFFRACTION99.32
2.86-3.040.32871320.27372513X-RAY DIFFRACTION99.74
3.04-3.280.3421310.2622486X-RAY DIFFRACTION99.81
3.28-3.60.28411310.19982496X-RAY DIFFRACTION99.32
3.6-4.130.18881340.16972541X-RAY DIFFRACTION99
4.13-5.20.18521340.14562547X-RAY DIFFRACTION99.89
5.2-36.310.22631410.18822665X-RAY DIFFRACTION99.82
Refinement TLS params.Method: refined / Origin x: -36.0799733663 Å / Origin y: 6.24140062516 Å / Origin z: 34.9150491804 Å
111213212223313233
T0.274525050478 Å20.000179239020463 Å2-0.0052422183402 Å2-0.265459612109 Å20.00937344494023 Å2--0.284137597138 Å2
L0.146937996436 °2-0.00155571952632 °20.0154604899225 °2--0.0559889703577 °20.0403025122945 °2--0.0334254709803 °2
S0.0111439477974 Å °-0.0414400356632 Å °0.00188350135126 Å °0.0271634850547 Å °0.0155615253902 Å °0.0228128144829 Å °-0.0268909998997 Å °-0.00228236383512 Å °-0.0259728989929 Å °
Refinement TLS groupSelection details: all

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