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- PDB-9gin: SOS2 in complex with compound 11 -

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Basic information

Entry
Database: PDB / ID: 9gin
TitleSOS2 in complex with compound 11
ComponentsSon of sevenless homolog 2
KeywordsHYDROLASE / SOS2 inhibitor cancer small molecule
Function / homology
Function and homology information


regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / positive regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / B cell homeostasis / regulation of T cell proliferation / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / positive regulation of small GTPase mediated signal transduction / NRAGE signals death through JNK / B cell homeostasis / regulation of T cell proliferation / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / insulin receptor signaling pathway / G alpha (12/13) signalling events / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol
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-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic 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-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic 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 / : / SOS1/NGEF-like PH 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. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
: / Son of sevenless homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsZak, K.M. / Kessler, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of Small Molecules that Bind to Son of Sevenless 2 (SOS2).
Authors: Zak, K.M. / Waterson, A.G. / Geist, L. / Braun, N. / Hauer, K. / Rumpel, K. / Ramharter, J. / Stadtmueller, H. / Wolkerstorfer, B. / Schoenbauer, D. / Cui, J. / Phan, J. / Abbott, J.R. / ...Authors: Zak, K.M. / Waterson, A.G. / Geist, L. / Braun, N. / Hauer, K. / Rumpel, K. / Ramharter, J. / Stadtmueller, H. / Wolkerstorfer, B. / Schoenbauer, D. / Cui, J. / Phan, J. / Abbott, J.R. / Sarkar, D. / Hodges, T.R. / Arnold, A. / Sensintaffar, J.L. / Fesik, S.W. / Kessler, D.
History
DepositionAug 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Son of sevenless homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7412
Polymers60,4921
Non-polymers2491
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area24410 Å2
Unit cell
Length a, b, c (Å)63.667, 85.075, 101.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Son of sevenless homolog 2 / SOS-2


Mass: 60492.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07890
#2: Chemical ChemComp-A1IL1 / ~{N}'-[2-nitro-4-(trifluoromethyl)phenyl]ethane-1,2-diamine


Mass: 249.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10F3N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-tris propane pH 8.0, 30 % PEG 3350, 0.2 M So-dium bromide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999891 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999891 Å / Relative weight: 1
ReflectionResolution: 2.06→65.2 Å / Num. obs: 24878 / % possible obs: 95 % / Redundancy: 13.2 % / Biso Wilson estimate: 44.33 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.2
Reflection shellResolution: 2.06→2.23 Å / Num. unique obs: 1245 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→53.91 Å / SU ML: 0.3094 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.4605
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 1265 5.09 %
Rwork0.2141 23606 -
obs0.2166 24871 71.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.13 Å2
Refinement stepCycle: LAST / Resolution: 2.06→53.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 17 185 3998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033921
X-RAY DIFFRACTIONf_angle_d0.55875300
X-RAY DIFFRACTIONf_chiral_restr0.0387574
X-RAY DIFFRACTIONf_plane_restr0.0049685
X-RAY DIFFRACTIONf_dihedral_angle_d16.88981526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.150.4887190.3804375X-RAY DIFFRACTION10.53
2.15-2.240.3565440.2921907X-RAY DIFFRACTION25.05
2.24-2.360.35031010.28061454X-RAY DIFFRACTION40.85
2.36-2.510.34851240.27742462X-RAY DIFFRACTION68.7
2.51-2.70.30341860.26163580X-RAY DIFFRACTION98.87
2.7-2.980.31422060.24863617X-RAY DIFFRACTION100
2.98-3.410.30822100.2233650X-RAY DIFFRACTION99.97
3.41-4.290.24311800.19183705X-RAY DIFFRACTION100
4.29-53.910.21761950.19293856X-RAY DIFFRACTION99.9
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)
12.79287454762-2.019441495831.494740678994.9508326182-2.193032884821.6188632712-0.432991579766-1.223541131080.2964912841640.8984516421020.358127516773-0.154421354175-0.185331362227-0.4486644139840.0537350986350.4891781169850.0875621440256-0.04019341629570.960350389632-0.03208505500550.41040244887618.6022920149-15.355531826827.0905462161
28.10603830113-3.82281372186-0.3346232018295.28862350787-0.7040106109364.786798574950.0628815201054-0.273436810871-0.201800757761-0.3153148222620.00550992957943-0.06232811673280.336470498238-0.0705463389466-0.03697989289720.305484699726-0.01563744146760.02545103294380.378106539640.07087320194960.22028423359116.7937013492-14.391477413913.7236235473
36.27794481447-3.758098708671.673036685122.14272076238-0.916770469210.5466772532220.7521577627861.54084176658-0.659434889241-0.67564558325-0.6804924258140.1718986524750.1687445790420.38952112825-0.1495128439250.9021445097060.1758223604440.03476885527680.86631938669-0.006242315188460.4766932478077.77581266795-13.2752331277-2.06138107609
47.6010044865-3.428658336230.09342685746634.233498918820.09369006966782.620565445650.3439291790930.426217454821-0.0237050566354-0.505798601817-0.2787190309380.08166256594910.1068417541390.0645038323317-0.06032615833790.2494899373620.00260109607066-0.02428161849230.2837104265410.02462076242960.229325259958-23.04275449328.25825739064.51171401978
56.48004393065-2.952263838551.020851798543.46986389812-0.8662586641491.68774912185-0.055200338247-0.748872590815-0.3163295993470.09787174296430.1892533297830.2905394259970.2324168525750.152772928952-0.119748137570.3663610318430.03833513832510.05598285523290.4945834182460.03260610064570.32460080087-15.2356356156-0.52358260486913.8789428647
66.27410951352-1.046068985171.02395033625.145689296250.2955707433562.713512286750.2325881714560.5012364374790.999233027948-0.389428708025-0.1284219568650.362498613911-0.38630649883-0.244380147609-0.1079100455230.3517855060770.04304828880670.02282867263730.5318693978950.06390818311170.559874529166-33.26582025721.38207590265.05508518361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 559 through 611 )559 - 6111 - 47
22chain 'A' and (resid 612 through 705 )612 - 70548 - 130
33chain 'A' and (resid 706 through 758 )706 - 758131 - 175
44chain 'A' and (resid 759 through 892 )759 - 892176 - 309
55chain 'A' and (resid 893 through 999 )893 - 999310 - 413
66chain 'A' and (resid 1000 through 1041 )1000 - 1041414 - 455

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