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- PDB-8un3: KRAS-G13D-GDP in complex with Cpd5 (1-((S)-10-(6-amino-4-methyl-3... -

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Basic information

Entry
Database: PDB / ID: 8un3
TitleKRAS-G13D-GDP in complex with Cpd5 (1-((S)-10-(6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl)-11-chloro-7-(((2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl)methoxy)-3,4,13,13a-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-2(1H)-yl)prop-2-en-1-one)
ComponentsGTPase KRas
KeywordsHYDROLASE / ONCOPROTEIN/INHIBITOR / GTPase / KRAS / G13D / oncogenic / ONCOPROTEIN-INHIBITOR complex
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / 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 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / positive regulation of glial cell proliferation / Signaling by FLT3 ITD and TKD mutants / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / mitochondrial outer membrane / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family 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 / Chem-XOI / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.07 Å
AuthorsUltsch, M.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Structure-Based Design and Evaluation of Reversible KRAS G13D Inhibitors.
Authors: Nilewski, C. / Labadie, S. / Wei, B. / Malhotra, S. / Do, S. / Gazzard, L. / Liu, L. / Shao, C. / Murray, J. / Izrayelit, Y. / Gustafson, A. / Endres, N.F. / Ma, F. / Ye, X. / Zou, J. / Evangelista, M.
History
DepositionOct 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,33023
Polymers76,6264
Non-polymers4,70419
Water7,746430
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3667
Polymers19,1561
Non-polymers1,2106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3466
Polymers19,1561
Non-polymers1,1905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2955
Polymers19,1561
Non-polymers1,1394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3225
Polymers19,1561
Non-polymers1,1664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.217, 69.217, 166.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 19156.496 Da / Num. of mol.: 4 / Fragment: GTPase, residues 2-168 / Mutation: G13D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, small monomeric GTPase

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Non-polymers , 6 types, 449 molecules

#2: Chemical
ChemComp-XOI / 1-[(5M,8aS,13R)-5-[6-amino-4-methyl-3-(trifluoromethyl)pyridin-2-yl]-6-chloro-2-{[(2S,4R)-4-fluoro-1-methylpyrrolidin-2-yl]methoxy}-8a,9,11,12-tetrahydropyrazino[2',1':3,4][1,4]oxazepino[5,6,7-de]quinazolin-10(8H)-yl]prop-2-en-1-one


Mass: 636.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H30ClF4N7O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 % / Mosaicity: 0.19 °
Crystal growTemperature: 277 K / Method: evaporation / pH: 8
Details: 0.2M Sodium Chloride, 0.1M Imidazole pH8.0, 0.4M Sodium di-hydrogen Phosphate, 1.6M Di-potassium Hydrogen Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.47
ReflectionResolution: 2.07→48.69 Å / Num. obs: 54585 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.046 / Rrim(I) all: 0.128 / Net I/σ(I): 12.3 / Num. measured all: 432438 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.07-2.138.11.1573477742860.4470.4341.2372.1100
9.02-48.697.90.04651946610.9990.0180.0535.199.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIXv1.2refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQA

4tqa


Resolution: 2.07→48.69 Å / Cross valid method: THROUGHOUT / σ(F): 2.24 / Phase error: 21.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1911 5196 4.77 %
Rwork0.1623 103771 -
obs0.166 54530 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.19 Å2 / Biso mean: 38.7432 Å2 / Biso min: 21.09 Å2
Refinement stepCycle: final / Resolution: 2.07→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5376 0 425 430 6231
Biso mean--36.01 40.98 -
Num. residues----672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.07-2.110.35262160.28375300551696
2.11-2.140.30072760.27225192546895
2.14-2.190.28283310.26615132546394
2.19-2.230.27712560.25445285554195
2.23-2.280.29582200.24585066528696
2.28-2.330.26082800.23665201548195
2.33-2.390.27712760.22585210548695
2.39-2.450.23873470.22435095544294
2.45-2.530.18931880.20575187537596
2.53-2.610.25552480.20465252550095
2.61-2.70.27671960.20065219541596
2.7-2.810.23252440.18715207545195
2.81-2.940.19972560.17765222547895
2.94-3.090.19973160.16225094541094
3.09-3.290.16982590.15955301556095
3.29-3.540.20032640.13955102536695
3.54-3.890.15222760.12765175545195
3.9-4.460.14452300.11285165539595
4.46-5.610.14163130.10765112542594
5.62-48.690.16471980.16165254545296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8677-2.945-0.56773.0168-0.91061.33380.01130.03280.81840.1754-0.0105-0.3055-0.19220.1147-0.09640.3677-0.02550.04090.191-0.01730.262112.22534.5274-3.11
22.89632.19320.73681.68170.95996.1195-0.02330.21570.72210.20640.06390.42090.094-0.16460.11870.4242-0.00560.05410.21330.04440.40716.076842.817-7.5642
36.53333.41396.45265.71594.51629.79290.1370.09090.2120.0260.1739-0.39740.17090.4212-0.01180.2922-0.02910.09410.2133-0.03150.373320.552136.4269-0.3764
47.5537-3.74510.75477.18531.75311.56250.18310.33480.2391-0.19880.0015-0.31380.3088-0.0309-0.11420.3564-0.0920.03820.3014-0.00220.200313.348825.1648-16.3353
53.80920.6918-0.94242.0821.66692.32360.29360.0547-0.02890.2422-0.21090.12740.0280.1232-0.15430.3571-0.0342-0.00980.20170.0040.16226.88922.356-3.6988
63.8282-0.369-1.48212.6968-0.07562.05560.2582-0.5340.16710.6445-0.17440.0602-0.13650.0899-0.11950.5099-0.09740.01720.3288-0.06080.19526.844328.22366.2063
71.9356-1.7222-0.12832.45530.99182.71970.0974-0.0294-0.26470.3068-0.13880.38760.164-0.08830.07350.3578-0.08140.06790.1685-0.04430.2875-11.4044-4.4935-2.8945
85.4386-0.48920.73885.2677-3.45432.30470.0380.4756-0.20850.2557-0.4095-0.86350.82770.08430.08750.56-0.129-0.03680.2252-0.10.3795-5.1099-11.595-8.8737
93.79540.3115-2.29271.8258-1.7493.57390.2578-0.0693-0.27570.1014-0.32930.5788-0.5699-0.26550.18380.4691-0.09770.1830.2244-0.03060.4335-19.3218-5.90560.5054
107.5652-2.2812-0.70577.3852-1.68893.70980.20020.1833-0.2228-0.60370.04640.0809-0.2195-0.1011-0.16170.3896-0.0628-0.01680.24480.00410.1829-13.60326.1478-15.4631
113.6843-1.21431.85442.4057-2.21242.54-0.04070.00480.13320.204-0.0091-0.1083-0.108-0.17980.02390.3701-0.00990.04410.1851-0.01870.1875-5.9098.3789-3.4084
122.235-1.2873-0.73583.8082-0.74361.7004-0.093-0.08520.03110.7749-0.0612-0.43240.30910.03820.09810.4966-0.031-0.05250.24080.02920.2341.42251.61575.6193
136.9097-4.02570.57724.71470.02414.2049-0.287-0.6005-0.08440.18740.35610.3704-0.212-0.1614-0.06430.4195-0.06340.09570.27190.02940.2619-15.93162.62026.7833
144.79962.0142-0.34833.2374-0.49062.28980.0868-0.04080.5878-0.09750.09550.255-0.2554-0.2832-0.12590.31010.02420.06250.19030.00090.2349-12.248634.5443-30.4162
154.5672-2.77482.58835.8099-5.43758.4281-0.2438-0.13140.6704-0.0309-0.3135-0.6686-0.38540.47980.42560.41680.01030.04760.2481-0.03350.3577-6.080842.8434-25.9675
168.3787-3.27235.93526.1353-4.1738.1841-0.0839-0.12520.6052-0.21520.11090.4418-0.0835-0.31530.22860.30470.03220.07050.18360.03670.3833-20.547136.4005-33.19
179.54192.5810.25058.3432-3.83413.99950.1128-0.53690.15880.52790.01040.2856-0.0822-0.0089-0.10810.32590.04090.01560.2585-0.01820.1522-13.361725.2045-17.264
185.6745-0.1787-1.1441.7733-1.15521.84870.25250.1335-0.1708-0.2123-0.1128-0.08220.049-0.159-0.18020.35550.0253-0.03150.2172-0.01560.1474-6.898822.3566-29.8396
194.9444.4596-0.93617.90451.05463.48930.06430.45310.0238-1.1904-0.081-0.3779-0.0940.1888-0.05540.51750.16890.09950.34610.08340.28682.048625.4684-39.9487
205.69082.5992-1.38564.9390.84291.878-0.10510.76920.4465-0.65190.1640.3332-0.2864-0.2577-0.04190.49720.0939-0.02150.37810.07120.1884-12.754730.0194-39.5966
213.11282.9367-1.35123.9953-1.62953.52520.1439-0.0679-0.3273-0.063-0.1305-0.2830.09640.19560.05980.30710.06270.03110.18760.03040.252311.4173-4.4885-30.6586
223.0908-0.4116-1.11784.33183.69943.35740.0829-0.2551-0.1639-0.2412-0.32130.7290.44730.1467-0.06860.5720.1137-0.04210.20320.06080.3725.1056-11.6216-24.6666
236.1302-1.4624-3.92941.72673.08336.55110.0407-0.062-0.4204-0.1968-0.1914-0.6597-0.09790.28820.5190.41730.03630.18440.20970.01840.440219.3494-5.887-34.0756
249.61693.99471.63927.88442.70453.59140.2056-0.1279-0.29850.71610.0186-0.17-0.17310.1992-0.26650.38890.0501-0.00410.2790.00360.169613.57436.1288-18.1101
256.58190.8060.87261.90760.98660.7629-0.0049-0.13910.0002-0.135-0.03590.1324-0.00180.07370.07070.366-00.04570.19210.01360.17244.31777.967-28.6404
268.01425.02443.20975.43454.2045.3885-0.79040.35920.0193-1.23750.28770.0944-0.27930.0090.43570.42730.0594-0.0060.2163-0.01840.25231.62423.8968-35.3589
272.2049-0.2493-0.56639.89931.04071.13190.14460.10320.0197-0.2637-0.22150.42350.44490.00550.1270.49420.0206-0.0170.2719-0.03170.14411.21943.2538-40.0045
289.536.77532.09618.5480.99174.355-0.52220.81240.116-1.01590.4182-0.3084-0.3530.39570.01790.40650.04120.10440.3199-0.01530.253915.90862.6524-40.3271
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 37 )A25 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 57 )A38 - 57
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 74 )A58 - 74
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 116 )A75 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 168 )A117 - 168
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 25 )B1 - 25
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 37 )B26 - 37
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 57 )B38 - 57
10X-RAY DIFFRACTION10chain 'B' and (resid 58 through 74 )B58 - 74
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 116 )B75 - 116
12X-RAY DIFFRACTION12chain 'B' and (resid 117 through 151 )B117 - 151
13X-RAY DIFFRACTION13chain 'B' and (resid 152 through 168 )B152 - 168
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 24 )C1 - 24
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 37 )C25 - 37
16X-RAY DIFFRACTION16chain 'C' and (resid 38 through 57 )C38 - 57
17X-RAY DIFFRACTION17chain 'C' and (resid 58 through 74 )C58 - 74
18X-RAY DIFFRACTION18chain 'C' and (resid 75 through 116 )C75 - 116
19X-RAY DIFFRACTION19chain 'C' and (resid 117 through 137 )C117 - 137
20X-RAY DIFFRACTION20chain 'C' and (resid 138 through 168 )C138 - 168
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 25 )D1 - 25
22X-RAY DIFFRACTION22chain 'D' and (resid 26 through 37 )D26 - 37
23X-RAY DIFFRACTION23chain 'D' and (resid 38 through 57 )D38 - 57
24X-RAY DIFFRACTION24chain 'D' and (resid 58 through 74 )D58 - 74
25X-RAY DIFFRACTION25chain 'D' and (resid 75 through 104 )D75 - 104
26X-RAY DIFFRACTION26chain 'D' and (resid 105 through 126 )D105 - 126
27X-RAY DIFFRACTION27chain 'D' and (resid 127 through 151 )D127 - 151
28X-RAY DIFFRACTION28chain 'D' and (resid 152 through 168 )D152 - 168

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