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- PDB-9qac: Crystal structure of the SMARCA2 bromodomain bound to a fragment ... -

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Basic information

Entry
Database: PDB / ID: 9qac
TitleCrystal structure of the SMARCA2 bromodomain bound to a fragment screening hit
ComponentsProbable global transcription activator SNF2L2
KeywordsGENE REGULATION / bromodomain / fragment screening hit
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
: / Probable global transcription activator SNF2L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSchimpl, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: ACS Medicinal Chemistry Letters / Year: 2025
Title: Discovery of Pyrimidoindolones as Novel Family VIII Bromo-domain Binders
Authors: Schimpl, M.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 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
C: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9089
Polymers43,1423
Non-polymers7676
Water46826
1
A: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6363
Polymers14,3811
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6363
Polymers14,3811
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6363
Polymers14,3811
Non-polymers2562
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.929, 65.929, 88.819
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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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: 14380.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 / Production host: Escherichia coli (E. coli)
References: UniProt: P51531, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-A1I5P / methyl 2-azanyl-1~{H}-indole-3-carboxylate


Mass: 190.199 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.07→57.096 Å / Num. obs: 13656 / % possible obs: 52 % / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.05 / Rrim(I) all: 0.112 / Net I/σ(I): 9
Reflection shellResolution: 2.071→2.343 Å / % possible obs: 8.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.797 / Num. measured all: 2578 / Num. unique obs: 684 / Rpim(I) all: 0.474 / Rrim(I) all: 0.931 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→48.03 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.553 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.457 / SU Rfree Blow DPI: 0.247 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.22 684 5.03 %RANDOM
Rwork0.188 ---
obs0.189 13595 51.7 %-
Displacement parametersBiso mean: 68.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.7231 Å20 Å20 Å2
2--1.7231 Å20 Å2
3----3.4463 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.07→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 45 26 2852
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012872HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043859HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes395HARMONIC5
X-RAY DIFFRACTIONt_it2872HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion18.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion369SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3131SEMIHARMONIC4
LS refinement shellResolution: 2.07→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.215 -2.6 %
Rwork0.192 300 -
all0.193 308 -
obs--5.69 %
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)
12.225-0.0182-1.17235.46222.85937.6466-0.2649-0.0740.0618-0.35150.1250.4797-0.2553-0.39460.1399-0.36250.0404-0.063-0.27330.0555-0.3239-6.378337.221512.2191
24.02220.6259-0.66074.3007-1.72516.5108-0.3268-0.3976-0.4497-0.26340.0044-0.40980.11150.43960.3223-0.37380.03320.1381-0.10890.0045-0.2807-29.259822.6114-10.3199
33.83770.5439-0.08765.0526-1.059413.5604-0.0580.1255-0.04440.1324-0.0404-0.08110.47810.81510.0985-0.17410.0403-0.1049-0.0857-0.0485-0.439-29.618553.6604-1.9786
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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