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- PDB-9qad: Crystal structure of the SMARCA2 bromodomain bound to a tricyclic... -

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Basic information

Entry
Database: PDB / ID: 9qad
TitleCrystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone inhibitor (compound 17)
ComponentsProbable global transcription activator SNF2L2
KeywordsGENE REGULATION / bromodomain / fragment screening / structure-based inhibitor design
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: 2.08 Å
AuthorsSchimpl, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2025
Title: Discovery of Pyrimidoindolones as Novel Family VIII Bromodomain Binders
Authors: Boerth, J.A. / Schimpl, M. / Lucas, S.C.C. / Zhang, J. / Code, E.L. / Embrey, K.J. / Rawlins, P.B. / Wang, H. / Storer, R.I. / Di Fruscia, P. / Nelson, J.E. / Milbradt, A.G. / Borjesson, U. ...Authors: Boerth, J.A. / Schimpl, M. / Lucas, S.C.C. / Zhang, J. / Code, E.L. / Embrey, K.J. / Rawlins, P.B. / Wang, H. / Storer, R.I. / Di Fruscia, P. / Nelson, J.E. / Milbradt, A.G. / Borjesson, U. / Gohlke, A. / Korboukh, V. / Gopalsamy, A.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 4, 2025Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop

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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)44,2129
Polymers43,1423
Non-polymers1,0706
Water72140
1
A: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7373
Polymers14,3811
Non-polymers3572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7373
Polymers14,3811
Non-polymers3572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7373
Polymers14,3811
Non-polymers3572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.023, 64.023, 88.985
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-A1I45 / 5-oxidanyl-2-(phenylmethyl)-1,9-dihydropyrimido[4,5-b]indol-4-one


Mass: 291.304 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H13N3O2 / 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.: 40 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 0.01 M ZnCl2, 12 % EG, 17 % PEG6000, 0.1 M Hepes pH 7

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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 / 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: 2.077→47.058 Å / Num. obs: 12801 / % possible obs: 52 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.032 / Rrim(I) all: 0.074 / Net I/σ(I): 13.4 / Num. measured all: 66212
Reflection shellResolution: 2.077→2.367 Å / % possible obs: 8 % / Redundancy: 5 % / Rmerge(I) obs: 0.919 / Num. measured all: 3182 / Num. unique obs: 638 / Rpim(I) all: 0.456 / Rrim(I) all: 1.028 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
MOSFLMdata reduction
Aimlessdata scaling
XDSdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.08→34.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.837 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.634 / SU Rfree Blow DPI: 0.29 / SU Rfree Cruickshank DPI: 0.303
RfactorNum. reflection% reflectionSelection details
Rfree0.245 620 4.88 %RANDOM
Rwork0.196 ---
obs0.198 12694 51.7 %-
Displacement parametersBiso mean: 62.29 Å2
Baniso -1Baniso -2Baniso -3
1-4.9611 Å20 Å20 Å2
2--4.9611 Å20 Å2
3----9.9221 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.08→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 69 40 2907
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012920HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043930HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1074SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it2920HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion18.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion372SEMIHARMONIC5
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_contact3288SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.31 Å / Total num. of bins used: 31
RfactorNum. reflection% reflection
Rfree0.2738 -5.12 %
Rwork0.2117 389 -
all0.2152 410 -
obs--6.2 %
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)
13.2026-0.38060.23823.8487-0.96935.858-0.09440.0251-0.2181-0.10510.36020.3010.2659-0.1758-0.2659-0.2195-0.0934-0.06050.20730.0538-0.229-3.208131.627912.5806
23.0040.08290.27662.2834-1.32746.4950.1836-0.10740.0343-0.1633-0.2517-0.1394-0.06630.26140.06810.1-0.13550.1158-0.00640.0092-0.2547-1.23394.7294-10.234
33.2636-0.1071-0.31633.04330.10334.957-0.0742-0.1695-0.0139-0.02240.01090.2121-0.12770.24760.06340.0038-0.14690.0560.0117-0.0969-0.2384-28.168919.928-2.3465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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