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- PDB-9ouj: K-Ras G12D 1-169 bound to MRTX-1133 at 310 K -

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Basic information

Entry
Database: PDB / ID: 9ouj
TitleK-Ras G12D 1-169 bound to MRTX-1133 at 310 K
ComponentsIsoform 2B of GTPase KRas
KeywordsHYDROLASE / GTPase
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / 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 / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / myoblast proliferation / 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 / RUNX3 regulates p14-ARF / skeletal muscle cell differentiation / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / cardiac muscle cell proliferation / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / glial cell proliferation / 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 / Signaling by CSF3 (G-CSF) / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / striated muscle cell differentiation / 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 / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / 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 / response to glucocorticoid / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / liver development / 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 / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / visual learning / regulation of long-term neuronal synaptic plasticity / 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 / DAP12 signaling / GDP binding / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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
Chem-6IC / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsXu, M. / Deck, S.L. / Milano, S.K. / Cerione, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA201402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124166 United States
CitationJournal: To Be Published
Title: Oncogenic Mutants of Ras bound to Inhibitors at Various Temperatures
Authors: Xu, M. / Deck, S.L. / Milano, S.K. / Cerione, R.A.
History
DepositionMay 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7528
Polymers38,6152
Non-polymers2,1366
Water1,18966
1
A: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3764
Polymers19,3081
Non-polymers1,0683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3764
Polymers19,3081
Non-polymers1,0683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.113, 52.586, 80.310
Angle α, β, γ (deg.)90.000, 91.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 1 through 117 or resid 119 through 203))
d_2ens_1(chain "B" and (resid 1 through 117 or resid 119 through 203))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11METMETLYSLYSAA1 - 1171 - 117
d_12ASPASPGDPGDPAA - E119 - 203119
d_136IC6IC6IC6ICAC201
d_21METMETLYSLYSBB1 - 1171 - 117
d_22ASPASPGDPGDPBB - H119 - 203119
d_236IC6IC6IC6ICBF201

NCS oper: (Code: givenMatrix: (-0.390875425218, 0.721386757242, -0.571679585464), (-0.1927535189, 0.543167372913, 0.81719966101), (0.90003471206, 0.429616516766, -0.0732609419054)Vector: 11. ...NCS oper: (Code: given
Matrix: (-0.390875425218, 0.721386757242, -0.571679585464), (-0.1927535189, 0.543167372913, 0.81719966101), (0.90003471206, 0.429616516766, -0.0732609419054)
Vector: 11.7003156242, 0.115290092763, -44.4250761537)

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Components

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


Mass: 19307.680 Da / Num. of mol.: 2 / Mutation: G12D, C51S, C80L, C118S
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, small monomeric GTPase
#2: Chemical ChemComp-6IC / 4-(4-[(1R,5S)-3,8-diazabicyclo[3.2.1]octan-3-yl]-8-fluoro-2-{[(2R,4R,7aS)-2-fluorotetrahydro-1H-pyrrolizin-7a(5H)-yl]methoxy}pyrido[4,3-d]pyrimidin-7-yl)-5-ethynyl-6-fluoronaphthalen-2-ol / MRTX-1133


Mass: 600.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H31F3N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.01 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 26% PEG8000, 150 mM ammonium acetate, 100 mM sodium citrate, pH 5.7

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Data collection

DiffractionMean temperature: 310 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.89→27.85 Å / Num. obs: 36882 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.6
Reflection shellResolution: 1.89→1.94 Å / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2686 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→27.85 Å / SU ML: 0.1789 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.2143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213 1982 5.38 %
Rwork0.205 34882 -
obs-36864 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.57 Å2
Refinement stepCycle: LAST / Resolution: 1.89→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2770 0 90 66 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01892926
X-RAY DIFFRACTIONf_angle_d2.00863982
X-RAY DIFFRACTIONf_chiral_restr0.0755436
X-RAY DIFFRACTIONf_plane_restr0.0102494
X-RAY DIFFRACTIONf_dihedral_angle_d18.03161120
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.890156138045 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.26071420.28822442X-RAY DIFFRACTION99.69
1.94-1.990.26011520.26462459X-RAY DIFFRACTION100
1.99-2.050.23361350.2352492X-RAY DIFFRACTION100
2.05-2.120.22941510.23552481X-RAY DIFFRACTION99.96
2.12-2.190.22651340.22822487X-RAY DIFFRACTION99.96
2.19-2.280.21971470.2342473X-RAY DIFFRACTION100
2.28-2.380.2071370.22862482X-RAY DIFFRACTION100
2.38-2.510.21711320.23592485X-RAY DIFFRACTION100
2.51-2.670.23281340.22862481X-RAY DIFFRACTION99.92
2.67-2.870.22251460.23992486X-RAY DIFFRACTION99.96
2.87-3.160.2421340.2232503X-RAY DIFFRACTION100
3.16-3.620.23691420.19972511X-RAY DIFFRACTION99.89
3.62-4.550.14881490.16872512X-RAY DIFFRACTION100
4.56-27.850.13471470.16652588X-RAY DIFFRACTION99.93

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