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- PDB-6v9f: Expanding the Chemical Landscape of SOS1 Activators Using Fragmen... -

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Basic information

Entry
Database: PDB / ID: 6v9f
TitleExpanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods
Components
  • (GTPase HRasHRAS) x 2
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / inhibitor / ONCOPROTEIN / Protein-protein complex / MAPK
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of miRNA metabolic process / T-helper 1 type immune response / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of wound healing / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / defense response to protozoan / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / adipose tissue development / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / molecular condensate scaffold activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Histone-fold / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-QTS / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsPhan, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten Foundation United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods.
Authors: Sarkar, D. / Olejniczak, E.T. / Phan, J. / Coker, J.A. / Sai, J. / Arnold, A. / Beesetty, Y. / Waterson, A.G. / Fesik, S.W.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: Son of sevenless homolog 1
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,66615
Polymers94,3783
Non-polymers1,28812
Water20,5731142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-40 kcal/mol
Surface area35680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.851, 183.851, 178.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2829-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18856.146 Da / Num. of mol.: 1 / Mutation: Y64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 56589.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07889
#3: Protein GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18932.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112

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Non-polymers , 7 types, 1154 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-QTS / 1-[(4-chlorophenyl)methyl]-1H-benzimidazol-2-amine


Mass: 257.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12ClN3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1142 / 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: 4 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4 / Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 128455 / % possible obs: 99.4 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.03 / Rrim(I) all: 0.108 / Χ2: 0.931 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.8811.71.17563320.7260.3541.2271.03298.7
1.88-1.9211.81.01963190.7770.3071.0651.06798.8
1.92-1.9511.90.84363240.8380.2530.8811.06698.9
1.95-1.9911.90.72463270.8840.2170.7561.06799
1.99-2.04120.58463400.910.1750.611.07999
2.04-2.08120.48863790.9410.1460.511.07599.1
2.08-2.1412.10.39363240.960.1170.411.05299.2
2.14-2.1912.20.33263700.9710.0990.3471.04899.3
2.19-2.2612.20.28463720.9790.0840.2961.01799.2
2.26-2.3312.30.24563740.9850.0720.2550.99699.3
2.33-2.4112.40.2163860.9880.0620.2191.0199.4
2.41-2.5112.40.18364370.9910.0540.1910.96399.6
2.51-2.6312.50.16264180.9920.0470.1690.96199.5
2.63-2.7612.60.1464240.9950.0410.1460.96599.6
2.76-2.9412.70.11364140.9960.0330.1180.94999.7
2.94-3.1612.60.08764950.9970.0250.0910.88699.8
3.16-3.4812.60.06164770.9980.0180.0640.82599.8
3.48-3.9912.60.04565250.9990.0130.0460.6799.9
3.99-5.0212.50.03565960.9990.010.0360.563100
5.02-5011.90.03868220.9990.0120.040.42199.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 1.849→41.11 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.99
RfactorNum. reflection% reflection
Rfree0.1707 2002 1.56 %
Rwork0.1568 --
obs0.157 128426 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.36 Å2 / Biso mean: 30.5621 Å2 / Biso min: 5.59 Å2
Refinement stepCycle: final / Resolution: 1.849→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 82 1150 7766
Biso mean--34.65 44.34 -
Num. residues----802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8494-1.89560.26071390.2348888099
1.8956-1.94690.2251350.2212890399
1.9469-2.00420.2651460.2015889499
2.0042-2.06880.19291410.1821892999
2.0688-2.14280.22061340.1693893399
2.1428-2.22860.2261460.162893699
2.2286-2.330.19391460.1618898599
2.33-2.45280.17261390.155900099
2.4528-2.60650.13891400.13899013100
2.6065-2.80770.17811490.15949039100
2.8077-3.09010.15661420.15619105100
3.0901-3.53710.14681450.14389129100
3.5371-4.45550.14111480.12839193100
4.4555-5.37290.16351520.15749485100
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)
12.18990.5651-0.11151.555-0.00373.30190.00660.0236-0.0626-0.02640.020.20810.0845-0.2017-0.03210.1514-0.04380.01530.1204-0.01340.155619.522450.176462.2692
24.15690.8019-4.84352.5326-1.52016.88260.0726-0.4186-0.11630.06-0.11-0.2081-0.15240.46280.09950.1909-0.0547-0.02380.2434-0.02110.157729.377245.141556.5491
33.19780.5447-0.94170.7838-0.77673.6637-0.0377-0.5506-0.21940.4629-0.09970.06130.42250.0280.15070.3989-0.08640.0250.310.01580.26522.687146.06173.9316
42.5431-1.62580.29773.6615-0.3711.94260.0214-0.48060.08430.40020.0609-0.0236-0.05490.1101-0.05420.2478-0.07910.02170.2682-0.0340.187127.582656.544774.1336
52.22940.79260.83641.31830.38861.72710.019-0.14120.3625-0.0213-0.050.2203-0.3276-0.03680.02790.2333-0.03390.05050.1579-0.02440.238924.561966.048965.6889
66.7568-3.81462.98034.9841-2.61554.74190.03890.2640.38810.1369-0.2619-0.456-0.20.60080.20080.2394-0.08520.03530.2408-0.0180.197834.291353.956760.3866
70.3016-0.273-0.24580.55170.43242.0582-0.0276-0.10070.02210.08750.019-0.01960.02780.15470.00160.1697-0.03440.00990.18130.00970.154215.497630.621879.8901
80.43850.2534-0.37830.2358-0.24551.65240.0384-0.01930.04770.0570.00370.0678-0.1935-0.111-0.05460.15790.0022-0.00020.1824-0.00890.20599.365840.185449.0029
90.41530.1029-0.10860.4795-0.1891.4103-0.04550.0642-0.0041-0.06860.0226-0.03290.0270.08980.02780.1373-0.02380.01730.1509-0.01270.159423.895633.061432.0215
102.9971-1.3255-0.79151.7437-0.12892.6257-0.0544-0.12460.29030.15040.0636-0.40550.00920.2816-0.01140.1989-0.0043-0.01450.1563-0.01710.28431.506212.122141.717
111.8083-2.98962.86184.9422-4.73114.52890.2219-0.2679-0.72790.57390.1934-0.21780.93670.235-0.21260.62570.0167-0.17910.31350.09940.725632.165412.631455.8324
124.4302-2.7471-2.63441.71041.57692.01230.1662-0.23030.3843-0.13850.0137-0.6666-0.27280.2878-0.14150.30940.0537-0.08850.37880.01120.495540.014914.237845.9069
131.1389-1.00690.89492.697-0.51531.70710.00030.14330.0054-0.0574-0.1342-0.36290.05010.15230.10420.1794-0.01420.02580.16310.00990.250229.369318.97936.1966
142.26521.033-1.27482.5246-1.41082.4120.10250.17440.0076-0.2655-0.03350.01080.05490.0529-0.07130.16930.03170.00580.1292-0.0210.15423.27598.710331.6959
155.1796-0.2502-2.89483.4599-0.18795.75870.0528-0.138-0.05740.026-0.04780.32750.2291-0.0558-0.00070.19010.004-0.02260.1533-0.03610.263118.0108-1.671936.3845
161.81780.76620.31952.8683-1.19633.01330.03570.0179-0.0149-0.0891-0.0751-0.2994-0.00260.15490.00520.16790.04510.01190.1463-0.01320.240232.39642.410939.6688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )A1 - 36
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )A37 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 74 )A53 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 116 )A75 - 116
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 151 )A117 - 151
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 166 )A152 - 166
7X-RAY DIFFRACTION7chain 'B' and (resid 565 through 699 )B565 - 699
8X-RAY DIFFRACTION8chain 'B' and (resid 700 through 818 )B700 - 818
9X-RAY DIFFRACTION9chain 'B' and (resid 819 through 1046 )B819 - 1046
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 24 )C0 - 24
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 34 )C25 - 34
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 48 )C35 - 48
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 74 )C49 - 74
14X-RAY DIFFRACTION14chain 'C' and (resid 75 through 117 )C75 - 117
15X-RAY DIFFRACTION15chain 'C' and (resid 118 through 137 )C118 - 137
16X-RAY DIFFRACTION16chain 'C' and (resid 138 through 166 )C138 - 166

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