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- PDB-9d11: Smarca2 Bromodomain in complex with compound 22 -

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Basic information

Entry
Database: PDB / ID: 9d11
TitleSmarca2 Bromodomain in complex with compound 22
ComponentsIsoform Short of Probable global transcription activator SNF2L2
KeywordsGENE REGULATION / Smarca2 / BRM / SWI/SNF / bromodomain
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
: / ACETATE ION / Probable global transcription activator SNF2L2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.684 Å
AuthorsMeagher, J.L. / Stuckey, J.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of High-Affinity SMARCA2/4 Bromodomain Ligands and Development of Potent and Exceptionally Selective SMARCA2 PROTAC Degraders.
Authors: Leng, L. / Tu, W. / Yang, L. / Huang, L. / Wang, M. / Meagher, J.L. / Chinnaswamy, K. / Allu, S.R. / Rej, R.K. / Tosovic, J. / Harikrishnan, L. / Li, Z. / Sui, Z. / Stuckey, J.A. / Wang, S.
History
DepositionAug 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 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: Isoform Short of Probable global transcription activator SNF2L2
B: Isoform Short of Probable global transcription activator SNF2L2
C: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,12315
Polymers43,3043
Non-polymers1,81912
Water3,891216
1
A: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1657
Polymers14,4351
Non-polymers7316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9794
Polymers14,4351
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isoform Short of Probable global transcription activator SNF2L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9794
Polymers14,4351
Non-polymers5443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.860, 60.860, 89.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Isoform Short of 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: 14434.527 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

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Non-polymers , 5 types, 228 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A1A1O / (12'S)-4'-chloro-10'-(piperidin-4-yl)-5'H-spiro[cyclohexane-1,7'-indolo[1,2-a]quinazolin]-5'-one


Mass: 419.946 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H26ClN3O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 32% Peg 3350, 50mM ZnAc, 6% Sucrose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 41720 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.034 / Rrim(I) all: 0.105 / Χ2: 0.831 / Net I/σ(I): 9.5 / Num. measured all: 381153
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.68-1.716.70.68521010.9080.9760.2840.7430.83699.5
1.71-1.747.60.73420610.9270.9810.2840.7880.8599.9
1.74-1.778.20.74720790.9370.9840.2750.7970.86299.8
1.77-1.818.60.65720900.9510.9870.2350.6980.88299.9
1.81-1.8590.57220690.9620.990.20.6070.864100
1.85-1.899.30.53521190.9730.9930.1840.5660.89199.9
1.89-1.949.30.4320680.9790.9950.1470.4550.905100
1.94-1.999.50.32620840.9830.9960.1110.3450.894100
1.99-2.059.30.25920860.9870.9970.0890.2740.92199.9
2.05-2.129.30.20621120.9880.9970.0710.2180.947100
2.12-2.198.90.15420840.9910.9980.0540.1630.92699.8
2.19-2.2880.12220830.990.9970.0460.1310.904100
2.28-2.389.90.10820840.9940.9980.0360.1140.878100
2.38-2.5110.10.09520940.9940.9990.0310.10.86799.9
2.51-2.6710.10.08220510.9950.9990.0270.0860.814100
2.67-2.8710.10.06921130.9950.9990.0230.0720.78899.8
2.87-3.16100.0620720.9960.9990.020.0640.751100
3.16-3.629.60.05521090.9960.9990.0180.0580.719100
3.62-4.568.70.04920710.9950.9990.0170.0520.63399.5
4.56-5010.80.04520900.9980.9990.0140.0480.55599.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.684→30.43 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.095 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.093
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2089 5.01 %RANDOM
Rwork0.1769 ---
obs0.1782 41672 99.8 %-
Displacement parametersBiso mean: 18.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.5059 Å20 Å20 Å2
2--0.5059 Å20 Å2
3----1.0119 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.684→30.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 117 217 3054
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092987HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.944110HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1101SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes575HARMONIC5
X-RAY DIFFRACTIONt_it2909HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion14.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion366SEMIHARMONIC5
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_contact3206SEMIHARMONIC4
LS refinement shellResolution: 1.684→1.7 Å
RfactorNum. reflection% reflection
Rfree0.2274 -6.71 %
Rwork0.203 778 -
obs--95.93 %
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)
10.59040.3008-0.0450.5352-0.00241.35970.0218-0.0004-0.03820.0478-0.0876-0.04780.03340.02370.0658-0.00730.0389-0.0135-0.02640.0046-0.0215-1.5005-4.8913-8.6731
20.89470.38960.61860.91360.21292.4752-0.005-0.02750.002-0.034-0.0086-0.0348-0.3846-0.06350.01360.002-0.00010.0144-0.02320.0019-0.0374-2.5509-29.1429-30.1275
31.11920.16280.3030.6716-0.07462.00380.0381-0.0021-0.1056-0.03770.0251-0.05510.00170.0201-0.06310.00840.0051-0.0163-0.0226-0.0253-0.0534-26.7536-21.1372-15.9816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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