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- PDB-4m22: Crystal Structure of small molecule acrylamide 16 covalently boun... -

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Basic information

Entry
Database: PDB / ID: 4m22
TitleCrystal Structure of small molecule acrylamide 16 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 / 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 / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / 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 / 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 / regulation of long-term neuronal synaptic plasticity / Constitutive Signaling by EGFRvIII / 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-22C / GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 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 5, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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)60,15111
Polymers58,0583
Non-polymers2,0938
Water2,774154
1
A: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8203
Polymers19,3531
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1664
Polymers19,3531
Non-polymers8133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: K-Ras GTPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1664
Polymers19,3531
Non-polymers8133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.906, 83.457, 86.924
Angle α, β, γ (deg.)90.000, 109.290, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-301-

HOH

21B-348-

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-22C / 1-{4-[(2,4-dichlorophenoxy)acetyl]piperazin-1-yl}propan-1-one


Mass: 345.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18Cl2N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG3000, 0.2M NaCl, 0.1M TRIS, pH 7.0, 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: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2011
Diffraction measurementDetails: 1.00 degrees, 5.0 sec, detector distance 250.00 mm / Method: \w scans
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionAv R equivalents: 0.08 / Number: 106533
ReflectionResolution: 2.09→25 Å / Num. obs: 28375 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 16.765
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 5.333 / Rsym value: 0.311 / % possible all: 100
Cell measurementReflection used: 106533

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å23.67 Å
Translation2.5 Å23.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
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: 2.09→23.673 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 1.37 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1989 7.02 %
Rwork0.179 --
obs0.1816 28329 99.46 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.42 Å2 / Biso mean: 41.3783 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: LAST / Resolution: 2.09→23.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 131 154 4033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093941
X-RAY DIFFRACTIONf_angle_d1.155350
X-RAY DIFFRACTIONf_chiral_restr0.06608
X-RAY DIFFRACTIONf_plane_restr0.004676
X-RAY DIFFRACTIONf_dihedral_angle_d16.261442
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 (%)
2.09-2.13880.2541250.20721790191595
2.1388-2.19660.2541510.20319192070100
2.1966-2.26120.23471510.18671816196799
2.2612-2.33410.21311320.185818671999100
2.3341-2.41750.26841360.190418972033100
2.4175-2.51420.22621440.186418822026100
2.5142-2.62850.2481510.189418992050100
2.6285-2.76680.21981380.204718601998100
2.7668-2.93990.24261290.202218962025100
2.9399-3.16640.24351530.197718802033100
3.1664-3.48420.22821450.180818902035100
3.4842-3.98620.2151490.172218992048100
3.9862-5.01440.15381450.145119142059100
5.0144-23.67480.19781400.16819312071100
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)
14.11672.2807-1.81967.0733-1.33052.66210.0755-0.4497-0.2801-0.3337-0.3368-0.8224-0.32660.88410.27510.2844-0.05130.01510.29770.04750.2243-5.04120.619712.8699
22.8822.85812.47473.24742.68412.3503-0.1179-0.4625-1.10210.04150.0614-1.39040.2290.93650.12610.48770.11110.10810.66040.260.81661.2897-8.134614.388
34.39543.1127-3.02082.2467-2.09752.16290.1051-0.0283-0.1822-0.7389-0.0348-0.546-0.93630.68320.95280.8252-0.11780.0930.4155-0.04290.2084-2.7837.89018.9414
40.9033-1.508-1.1999.0045.18593.1518-0.1514-0.14280.62250.31890.9177-1.35950.06390.9397-0.69460.4863-0.0796-0.02780.6065-0.17560.4518-6.67797.190423.0455
53.94552.6176-1.58455.8646-1.27453.870.0636-0.20970.05860.3378-0.08250.24840.03670.07540.05720.2062-0.00440.01150.24270.01290.1495-17.033-4.003417.811
64.75691.3892-1.7654.2462-0.27193.3779-0.35880.37290.1238-0.77470.24520.221-0.212-0.23850.05720.40670.0114-0.03620.26160.0170.1697-16.90780.63398.3097
75.75650.1159-2.63995.0882-1.19644.46010.0821-0.21840.41240.40530.01430.2029-0.1736-0.2586-0.07040.1927-0.0009-0.02320.2539-0.04380.13854.369927.996443.3205
83.9286-2.54752.03355.7402-2.33722.8542-0.4369-0.58490.80510.54570.1415-0.2458-0.7763-0.2790.28870.37870.0454-0.06680.2697-0.08260.472912.113434.803343.0888
98.4315-0.2317-2.2443.58980.84173.4111-0.0091-0.50920.13930.4559-0.14780.1204-0.0381-0.40570.09850.3327-0.0049-0.02660.3403-0.0620.17255.91221.391247.9695
103.167-0.4933-0.79914.9358-2.3555.1785-0.06990.1755-0.3997-0.1326-0.15350.03980.5482-0.27650.18910.1934-0.0628-0.00290.2707-0.05760.1674.919617.504234.6236
113.87510.99460.1374.9658-0.37063.1787-0.13560.21160.4334-0.09530.03230.4069-0.2463-0.67670.07670.16940.0615-0.03580.4541-0.00820.2816-2.359426.225232.6324
124.5303-2.5154-1.16776.99751.01336.3706-0.0511-0.5186-0.98320.28490.2769-0.42830.83730.3953-0.14070.29370.0244-0.0280.2930.03310.41122.8047-0.077119.5182
137.72475.8036-2.2652.00392.32053.50490.7057-1.3073-0.3520.6262-0.1172-0.29380.80631.0876-0.50640.714-0.0545-0.11860.62310.16090.748419.90150.011128.9626
143.57252.59821.42616.7853.49964.0387-0.04980.3342-1.15150.43340.1358-0.36410.65990.5834-0.11230.52990.08420.05930.3676-0.08630.794525.0725-7.890115.4013
157.85272.52522.83422.3428-0.66085.01440.6719-0.61461.0699-0.3218-0.0572-0.9813-0.5510.8986-0.46350.3095-0.03120.05380.5941-0.07280.948535.9175.5618.6046
165.2711-0.4975-1.10963.54220.45443.07970.30310.17080.1055-0.5265-0.0372-0.8103-0.49810.3912-0.25580.3436-0.05160.11630.3264-0.00550.35625.16112.91414.7497
177.41630.62650.42484.04160.252.74650.31580.3743-0.1696-0.4456-0.1846-0.0911-0.375-0.108-0.11410.3038-0.01390.03730.2218-0.00040.195216.605110.244314.0117
185.0058-0.8795-1.54035.98710.40346.272-0.02870.5525-0.5989-0.56550.0456-0.02720.0173-0.08920.01170.3082-0.0641-0.00810.3146-0.09350.276717.70254.24718.7601
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 37 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 57 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 58 through 76 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 126 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 168 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 25 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 37 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 74 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 75 through 116 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 167 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 25 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 26 through 37 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 38 through 57 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 58 through 74 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 104 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 105 through 126 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 127 through 168 )C0

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