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- PDB-9ayq: SMARCA2 in complex with a pyridine-2-one-based inhibitor -

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Basic information

Entry
Database: PDB / ID: 9ayq
TitleSMARCA2 in complex with a pyridine-2-one-based inhibitor
ComponentsProbable global transcription activator SNF2L2
KeywordsDNA BINDING PROTEIN / Helicase
Function / homology
Function and homology information


bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / nucleosome array spacer activity / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / intermediate filament cytoskeleton / SWI/SNF complex ...bBAF complex / npBAF complex / nBAF complex / brahma complex / GBAF complex / nucleosome array spacer activity / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / intermediate filament cytoskeleton / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / positive regulation of double-strand break repair / spermatid development / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / helicase activity / positive regulation of cell differentiation / negative regulation of cell growth / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nervous system development / histone binding / transcription coactivator activity / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain ...BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / ADENOSINE-5'-DIPHOSPHATE / Probable global transcription activator SNF2L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.9 Å
AuthorsFarrow, N.A. / Cocozaki, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Discovery of a SMARCA2/4 ATPase Inhibitors Suitable for Use in SMARCA4-mutant Preclinical Models
Authors: Alford, J. / Farrow, N.A.
History
DepositionMar 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable global transcription activator SNF2L2
B: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,4166
Polymers161,7712
Non-polymers1,6454
Water1086
1
A: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7083
Polymers80,8861
Non-polymers8222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7083
Polymers80,8861
Non-polymers8222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.106, 63.967, 126.575
Angle α, β, γ (deg.)90.00, 102.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable global transcription activator SNF2L2 / ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / ...ATP-dependent helicase SMARCA2 / BRG1-associated factor 190B / BAF190B / Protein brahma homolog / hBRM / SNF2-alpha / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2


Mass: 80885.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-A1AHQ / 4-cyano-N-[1-(2,2-difluoroethyl)-5-fluoro-6-oxo-1,6-dihydropyridin-3-yl]-5-(trifluoromethyl)thiophene-2-carboxamide


Mass: 395.280 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H7F6N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 uL of protein at a concentration of 28.5 mg/ml in a buffer 25mM Hepes, 300mM NaCl, 5% glycerol, 1mM TCEP, pH 7.5 was combined with 1ul of 0.1 M HEPES, pH 7.1, 4% w/v PEG 8000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.9→47.24 Å / Num. obs: 29989 / % possible obs: 86.8 % / Redundancy: 2.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.067 / Rrim(I) all: 0.12 / Χ2: 1.05 / Net I/σ(I): 8
Reflection shellResolution: 2.9→3.06 Å / % possible obs: 89.9 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.504 / Num. measured all: 11926 / Num. unique obs: 4505 / CC1/2: 0.819 / Rpim(I) all: 0.347 / Rrim(I) all: 0.615 / Χ2: 0.97 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.9→47.24 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.89 / SU B: 30.091 / SU ML: 0.503 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2867 1370 4.9 %RANDOM
Rwork0.23179 ---
obs0.2345 26515 79.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.394 Å2
Baniso -1Baniso -2Baniso -3
1-6.33 Å20 Å23.98 Å2
2---8.17 Å20 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.9→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9522 0 106 6 9634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139804
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159515
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.65613214
X-RAY DIFFRACTIONr_angle_other_deg1.0551.5821870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37651140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85321.394574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.954151888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9261591
X-RAY DIFFRACTIONr_chiral_restr0.0460.21260
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210793
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1296.9494596
X-RAY DIFFRACTIONr_mcbond_other3.1286.9484595
X-RAY DIFFRACTIONr_mcangle_it5.1710.4085724
X-RAY DIFFRACTIONr_mcangle_other5.1710.4085725
X-RAY DIFFRACTIONr_scbond_it2.8497.1755208
X-RAY DIFFRACTIONr_scbond_other2.8467.1835154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.88310.657411
X-RAY DIFFRACTIONr_long_range_B_refined7.62877.64310512
X-RAY DIFFRACTIONr_long_range_B_other7.62277.76310437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 18351 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 111 -
Rwork0.399 1963 -
obs--81.72 %

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