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- PDB-9pvf: KRAS complex with UM0152533 compound -

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Basic information

Entry
Database: PDB / ID: 9pvf
TitleKRAS complex with UM0152533 compound
Components
  • GTPase KRas
  • UM0152533
KeywordsHYDROLASE/INHIBITOR / GTPase / Inhibitor / Macrocycle / SIGNALING PROTEIN / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / skeletal muscle cell differentiation / Rac protein signal transduction / myoblast proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / cardiac muscle cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / homeostasis of number of cells within a tissue / 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 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / striated muscle cell differentiation / 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 / 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 / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / liver development / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / female pregnancy / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / RAF activation / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / visual learning / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / Signaling by RAF1 mutants / Signaling by CSF1 (M-CSF) in myeloid cells / 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 / positive regulation of cellular senescence / Signaling by BRAF and RAF1 fusions / GDP binding / DAP12 signaling / MAPK cascade / neuron apoptotic process
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 KRas
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 KRas
B: GTPase KRas
C: GTPase KRas
D: GTPase KRas
E: GTPase KRas
F: GTPase KRas
I: UM0152533
J: UM0152533
K: UM0152533
L: UM0152533
M: UM0152533
N: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,58631
Polymers122,61112
Non-polymers2,97519
Water11,836657
1
A: GTPase KRas
I: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9275
Polymers20,4352
Non-polymers4923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-30 kcal/mol
Surface area8450 Å2
MethodPISA
2
B: GTPase KRas
J: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9275
Polymers20,4352
Non-polymers4923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-30 kcal/mol
Surface area8350 Å2
MethodPISA
3
C: GTPase KRas
K: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9275
Polymers20,4352
Non-polymers4923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-30 kcal/mol
Surface area8560 Å2
MethodPISA
4
D: GTPase KRas
L: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9275
Polymers20,4352
Non-polymers4923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-29 kcal/mol
Surface area8130 Å2
MethodPISA
5
E: GTPase KRas
M: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9275
Polymers20,4352
Non-polymers4923
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-31 kcal/mol
Surface area8360 Å2
MethodPISA
6
F: GTPase KRas
N: UM0152533
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9516
Polymers20,4352
Non-polymers5164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-30 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.640, 99.640, 140.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

#1: Protein
GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 18884.285 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116
#2: Protein/peptide
UM0152533


Mass: 1550.842 Da / Num. of mol.: 6 / 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.: 6 / 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.: 13 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 3.08 Å3/Da / Density % sol: 60.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 0.1 M Bis-Tris, 0.2 M MgCl2, 25 % 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: 2→40.66 Å / Num. obs: 92437 / % possible obs: 99.97 % / Redundancy: 6.7 % / Biso Wilson estimate: 32.76 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08753 / Rpim(I) all: 0.03653 / Rrim(I) all: 0.09797 / Net I/σ(I): 14.56
Reflection shellResolution: 2→2.071 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 2.09 / Num. unique obs: 9226 / CC1/2: 0.641 / CC star: 0.884 / Rpim(I) all: 0.4349 / Rrim(I) all: 1.146 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.66 Å / SU ML: 0.2179 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1118
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2155 4623 5 %
Rwork0.1758 87814 -
obs0.1778 92437 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.33 Å2
Refinement stepCycle: LAST / Resolution: 2→40.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 797 657 9389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088938
X-RAY DIFFRACTIONf_angle_d1.312412141
X-RAY DIFFRACTIONf_chiral_restr0.05641309
X-RAY DIFFRACTIONf_plane_restr0.011521
X-RAY DIFFRACTIONf_dihedral_angle_d23.34281287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.28131530.25312912X-RAY DIFFRACTION100
2.02-2.050.3191550.2372930X-RAY DIFFRACTION100
2.05-2.070.31481530.24062920X-RAY DIFFRACTION100
2.07-2.10.24421540.22222922X-RAY DIFFRACTION100
2.1-2.130.25331540.21732924X-RAY DIFFRACTION100
2.13-2.150.2671520.21082892X-RAY DIFFRACTION100
2.15-2.190.25391550.21262940X-RAY DIFFRACTION100
2.19-2.220.22751550.2072947X-RAY DIFFRACTION100
2.22-2.250.23411520.18612886X-RAY DIFFRACTION100
2.25-2.290.26321520.18342892X-RAY DIFFRACTION100
2.29-2.330.24311540.18112931X-RAY DIFFRACTION99.97
2.33-2.370.21541570.17222966X-RAY DIFFRACTION100
2.37-2.420.25561520.17432893X-RAY DIFFRACTION100
2.42-2.470.21231550.18032943X-RAY DIFFRACTION100
2.47-2.520.23951530.17342909X-RAY DIFFRACTION100
2.52-2.580.23741540.16682918X-RAY DIFFRACTION99.93
2.58-2.640.24521520.16812904X-RAY DIFFRACTION100
2.64-2.710.2061560.17232949X-RAY DIFFRACTION100
2.71-2.790.22761520.18322891X-RAY DIFFRACTION100
2.79-2.880.21361550.1872946X-RAY DIFFRACTION100
2.88-2.990.24831530.1722919X-RAY DIFFRACTION100
2.99-3.110.23561550.182937X-RAY DIFFRACTION100
3.11-3.250.20781540.1782935X-RAY DIFFRACTION100
3.25-3.420.22661560.1742949X-RAY DIFFRACTION99.94
3.42-3.630.21151530.17192908X-RAY DIFFRACTION100
3.63-3.910.21550.15912946X-RAY DIFFRACTION100
3.91-4.310.16061540.14552923X-RAY DIFFRACTION100
4.31-4.930.1571560.13772959X-RAY DIFFRACTION99.87
4.93-6.210.18651550.17792949X-RAY DIFFRACTION99.97
6.21-40.660.23321570.19682974X-RAY DIFFRACTION99.78
Refinement TLS params.Method: refined / Origin x: 5.72096899804 Å / Origin y: -30.1370305992 Å / Origin z: 20.5749665609 Å
111213212223313233
T0.237739637176 Å2-0.00205368061151 Å2-0.0206969592398 Å2-0.245945110037 Å2-0.0226633778682 Å2--0.241012528918 Å2
L0.157843378831 °2-0.10166195758 °20.00891348366989 °2-0.0446073999827 °20.0334435589735 °2--0.0686084008942 °2
S0.00165142150343 Å °-0.0129588796549 Å °-0.027885062859 Å °-0.016924191702 Å °0.00200523054083 Å °0.0132919495116 Å °0.0406599079018 Å °-0.0155267060687 Å °-0.00639875744205 Å °
Refinement TLS groupSelection details: all

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