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- PDB-4m1y: Crystal Structure of small molecule vinylsulfonamide 15 covalentl... -

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Basic information

Entry
Database: PDB / ID: 4m1y
TitleCrystal Structure of small molecule vinylsulfonamide 15 covalently bound to K-Ras G12C
ComponentsK-Ras GTPase
KeywordsSIGNALING PROTEIN/INHIBITOR / GTPase / GDP bound / small molecule inhibitor / covalent binder / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / Signaling by CSF3 (G-CSF) / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / homeostasis of number of cells within a tissue / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / G protein activity / cytoplasmic side of plasma membrane / Signaling by CSF1 (M-CSF) in myeloid cells / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / 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 nucleotide triphosphate hydrolases ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-21S / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.491 Å
AuthorsOstrem, J.M. / Peters, U. / Sos, M.L. / Wells, J.A. / Shokat, K.M.
CitationJournal: Nature / Year: 2013
Title: K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions.
Authors: Ostrem, J.M. / Peters, U. / Sos, M.L. / Wells, J.A. / Shokat, K.M.
History
DepositionAug 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: K-Ras GTPase
B: K-Ras GTPase
C: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8407
Polymers58,0583
Non-polymers1,7824
Water5,657314
1
A: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7962
Polymers19,3531
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2483
Polymers19,3531
Non-polymers8962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7962
Polymers19,3531
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.121, 83.540, 86.224
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-374-

HOH

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Components

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


Mass: 19352.785 Da / Num. of mol.: 3 / Fragment: UNP residues 1-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS isoform 2B, KRAS2, RASK2 / Plasmid: pJexpress411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01116
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-21S / N-{1-[N-(5,7-dichloro-2,1,3-benzothiadiazol-4-yl)glycyl]piperidin-4-yl}ethanesulfonamide


Mass: 452.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19Cl2N5O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IN THE STRUCTURE REPRESENTS ISOFORM 2B OF GTPASE KRAS. THIS ISOFORM DIFFERS FROM THE ...THE SEQUENCE IN THE STRUCTURE REPRESENTS ISOFORM 2B OF GTPASE KRAS. THIS ISOFORM DIFFERS FROM THE CANONICAL SEQUENCE AS FOLLOW: 151-153 (RVE TO GVD) AND 165-169 (QYRLK TO KHKEK)

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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: 1.97 Å3/Da / Density % sol: 37.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 31% PEG4000, 0.2M NH4CH3COO, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2012
Diffraction measurementDetails: 1.00 degrees, 1.5 sec, detector distance 175.00 mm / Method: \w scans
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.031 / Number: 269532
ReflectionResolution: 1.49→25 Å / Num. obs: 71411 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.031 / Rsym value: 0.031 / Net I/σ(I): 31.189
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.673 / Rsym value: 0.381 / % possible all: 96.2
Cell measurementReflection used: 269532

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.49 Å23.38 Å
Translation1.49 Å23.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.0phasing
PHENIXdev_1402refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GFT

3gft


Resolution: 1.491→23.379 Å / Occupancy max: 1 / Occupancy min: 0.14 / SU ML: 0.13 / σ(F): 1.34 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1908 1999 2.8 %
Rwork0.1668 --
obs0.1675 71402 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.03 Å2 / Biso mean: 39.667 Å2 / Biso min: 13.12 Å2
Refinement stepCycle: LAST / Resolution: 1.491→23.379 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 111 314 4140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083920
X-RAY DIFFRACTIONf_angle_d1.1945316
X-RAY DIFFRACTIONf_chiral_restr0.063605
X-RAY DIFFRACTIONf_plane_restr0.005666
X-RAY DIFFRACTIONf_dihedral_angle_d17.7511469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4914-1.52870.23661340.21794721485594
1.5287-1.570.22861460.20484919506597
1.57-1.61620.21451340.19494917505197
1.6162-1.66840.19321380.18224953509197
1.6684-1.7280.20211470.18614924507197
1.728-1.79710.20591520.18224975512798
1.7971-1.87890.2131440.17514946509098
1.8789-1.97790.19461390.17315002514198
1.9779-2.10180.18111450.16775010515598
2.1018-2.26390.1791480.1635028517699
2.2639-2.49150.1951420.16255014515699
2.4915-2.85150.19311460.16895095524199
2.8515-3.59050.17011470.15875080522799
3.5905-23.38180.19561370.164819495693
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)
14.4215-0.82051.93525.4009-1.28773.28720.1288-0.0838-0.2082-0.1004-0.1468-0.50940.30240.46860.07170.12890.03870.02130.25830.00990.174735.622116.9562148.4035
27.8031-2.3676-1.57964.16454.0344.04290.18510.3481.1398-1.65590.5853-0.8202-0.17390.1412-0.48030.6511-0.1056-0.01350.54750.10130.628941.687426.6604151.102
31.11780.35410.37425.9329-2.45582.10110.250.16850.18190.0904-0.2255-0.0637-0.07140.3866-0.0060.26010.05620.02040.38550.02380.232138.22310.2094151.9911
47.6565-0.54320.46328.6362-0.01897.6964-0.07230.93090.91850.15060.025-1.2782-0.4840.94670.07840.58570.02150.01020.5611-0.05480.624436.324513.2858134.7906
52.4203-1.16940.50492.5553-0.28082.44780.31350.3759-0.4585-0.7378-0.1750.4260.28990.10970.01960.24410.0393-0.08470.1451-0.07250.209523.658919.8005140.7844
63.2041-0.70470.80763.2003-0.79782.59770.08320.0386-0.2330.00610.02960.20.13150.0298-0.0360.1303-0.0056-0.01460.1196-0.00360.153323.442322.1974148.0935
73.6782-1.40421.43224.3314-0.58372.5372-0.016-0.195-0.36080.16720.09040.3260.156-0.033-0.03950.1811-0.00870.02330.18390.01990.189123.762416.5672153.1675
83.3429-0.4279-0.09264.32890.23232.8349-0.0761-0.32980.72780.03380.0790.386-0.5893-0.1989-0.10240.27460.0390.0190.1416-0.03750.29119.733618.285179.8471
93.5081-1.75160.49970.87460.01982.83850.1636-0.36940.47550.58820.31060.1223-1.4334-0.4119-0.41090.7213-0.02730.13630.3249-0.01970.654823.050425.2725179.8156
107.29680.9757-2.05155.3796-3.16498.67910.0577-0.3896-0.01090.68220.10530.3065-0.5764-0.7633-0.2780.35120.0575-0.04350.3989-0.10360.559413.29918.6976181.0809
115.3474-0.20341.59681.15590.15912.0092-0.0601-0.3967-0.0323-0.10830.02840.8686-0.1124-0.55990.02490.1780.0421-0.02090.24760.02030.416811.281311.1376177.8334
123.4048-2.66933.05144.2778-1.20984.40210.1044-0.1698-0.5166-0.2140.06160.77820.1319-0.3018-0.09630.1509-0.002-0.01360.14860.02040.253317.57771.6386176.1246
134.5031-0.38330.00615.2505-0.29382.92670.13580.24120.1153-0.3155-0.13520.17130.10490.06690.03050.17810.01490.01270.11490.02140.114424.92427.0068175.1603
143.24580.81834.33276.62941.90076.70220.20470.2377-0.5603-0.65830.1377-0.23340.17360.5846-0.27180.28880.00340.04080.24760.00760.160827.31071.4059167.2771
153.78033.08334.58244.17184.74746.1565-0.11530.42280.2336-0.40720.3236-0.5266-0.51650.6127-0.20880.2481-0.02320.00920.19550.02270.247230.300913.0372175.6355
167.62740.2271.26443.7119-1.23492.66740.05811.15380.636-0.9912-0.11080.272-0.3894-0.06230.22120.45430.0703-0.05270.29640.07460.305420.391519.1437166.9633
171.2755-0.95271.7952.8784-0.46644.0553-0.1312-1.2829-0.73630.7147-0.06490.10670.3402-0.1938-0.28670.34860.06010.01130.61540.22970.23126.127729.708203.7878
182.0560.76750.12586.8646-0.18553.24580.0582-1.0108-0.40590.7688-0.0270.8308-0.0495-0.1903-0.03340.51610.02810.02410.7920.14380.42378.800332.3129208.0529
194.29951.38322.2214.57882.10797.0484-0.231-0.62540.24260.10310.0840.3329-0.7533-0.33970.17260.21990.05720.00230.2123-0.01760.12971.685339.6036193.6629
206.58541.50932.1096.0425-0.83194.3249-0.16030.0567-0.1947-0.12850.0331-0.3474-0.20880.05530.07230.14150.00670.02010.1710.020.13058.506435.8074189.2499
217.45261.94623.71795.41372.88537.0283-0.0615-0.4899-0.54490.50060.2171-0.25980.14620.5532-0.0580.24310.0263-0.04890.34280.1260.285614.764430.8054199.2061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 38 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 58 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 74 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 103 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 126 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 168 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 25 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 48 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 64 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 83 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 84 through 103 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 104 through 126 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 127 through 137 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 138 through 151 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 152 through 169 )B0
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 25 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 26 through 76 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 77 through 103 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 104 through 143 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 144 through 167 )C0

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