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- PDB-7vsf: crystal structure of BRD2-BD1 in complex with purine derivative -

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Basic information

Entry
Database: PDB / ID: 7vsf
Titlecrystal structure of BRD2-BD1 in complex with purine derivative
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION/INHIBITOR / BET family / BET inhibitor / Bromodomain Inhibitor / BRD2-BD1 inhibitor / TRANSCRIPTION-INHIBITOR COMPLEX
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
3-methyl-7-propyl-purine-2,6-dione / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPadmanabhan, B. / Arole, A. / Deshmukh, P. / Ashok, S. / Mathur, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural and biochemical insights into purine-based drug molecules in hBRD2 delineate a unique binding mode opening new vistas in the design of inhibitors of the BET family.
Authors: Arole, A.H. / Deshmukh, P. / Sridhar, A. / Mathur, S. / Mahalingaswamy, M. / Subramanya, H. / Dalavaikodihalli Nanjaiah, N. / Padmanabhan, B.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6158
Polymers44,6563
Non-polymers9595
Water1,36976
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5216
Polymers29,7712
Non-polymers7514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-14 kcal/mol
Surface area11210 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1874
Polymers29,7712
Non-polymers4162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2530 Å2
ΔGint-36 kcal/mol
Surface area10960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.947, 55.550, 67.281
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Bromodomain-containing protein 2


Mass: 14885.340 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-7UM / 3-methyl-7-propyl-purine-2,6-dione


Mass: 208.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG MME 5000, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Dec 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14540 / % possible obs: 99.81 % / Redundancy: 4.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.121 / Net I/σ(I): 6.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.899 / Num. unique obs: 1615 / CC1/2: 0.53 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.18_3855: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JKE

6jke


Resolution: 2.5→23.57 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2553 779 5.36 %
Rwork0.2011 --
obs0.2041 14540 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→23.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2658 0 65 76 2799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092808
X-RAY DIFFRACTIONf_angle_d0.9823818
X-RAY DIFFRACTIONf_dihedral_angle_d5.61395
X-RAY DIFFRACTIONf_chiral_restr0.05402
X-RAY DIFFRACTIONf_plane_restr0.006519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.660.37921200.30912256X-RAY DIFFRACTION100
2.66-2.860.37581390.26882292X-RAY DIFFRACTION100
2.86-3.150.33331100.25562288X-RAY DIFFRACTION100
3.15-3.60.30911430.22412259X-RAY DIFFRACTION100
3.6-4.530.1931470.16072301X-RAY DIFFRACTION100
4.53-23.570.20241200.16362365X-RAY DIFFRACTION100
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)
10.7671-0.20330.22940.16180.11030.26560.7845-0.3239-0.86530.64620.650.8877-0.5415-0.65050.01930.37410.12470.29140.58880.20210.48968.7786-3.450510.2167
21.04620.8177-0.07050.66490.27890.44930.11751.0334-0.4652-0.0391-0.43360.28210.024-0.4324-0.00220.49560.0951-0.03980.4818-0.04080.470315.4905-0.923-9.4011
30.2728-0.53970.21680.4277-0.42260.5449-0.28060.0885-0.7544-0.0713-0.04370.55380.2616-0.4437-0.00090.3675-0.0360.04030.36070.00370.597814.8334-9.9919-3.1633
40.25760.21820.07360.18510.07050.0697-0.5287-0.8971-1.43090.19930.3819-0.01270.0871-0.7851-0.00860.48980.01640.20510.69390.23731.18998.9745-15.19688.5945
52.8449-1.70010.80462.91560.6041.19850.0733-0.0421-0.2-0.08060.14490.1914-0.1063-0.2801-0.00070.3042-0.02430.0290.3158-0.0070.398122.819-5.1626-0.932
61.717-1.19680.04971.37060.4310.595-0.3919-0.37060.0870.34740.20780.1991-0.50650.0082-0.00650.40080.05170.040.3476-0.00030.42119.45782.00276.4423
72.6264-0.38641.83352.6035-0.36081.2502-0.087-0.220.15430.37530.0589-0.39840.0080.06730.00010.44390.036-0.05340.37310.00610.346837.0775-5.14413.979
81.0656-0.52760.54351.9057-0.05680.6602-0.4475-0.26060.56230.5782-0.0105-0.8013-0.59250.1203-0.00180.4662-0.0193-0.12060.39810.0010.515538.75013.60957.0818
90.0707-0.002-0.07470.0489-0.01970.04150.449-0.70340.31470.7811-0.20950.0736-0.75190.655101.08210.1193-0.12310.6137-0.11180.583132.27498.185121.1464
102.16260.04511.34282.3151-1.62221.89-0.0051-0.29460.20030.43610.3174-0.4664-0.13430.2184-00.45340.02780.00080.2449-0.00060.343431.776-1.55034.5796
111.8047-0.16091.62130.84820.13871.2788-0.3085-0.7065-0.55860.04690.02450.2788-0.1118-0.0445-0.00040.37240.02510.06470.36880.04410.400227.4727-8.948911.0464
120.49160.5496-0.15870.8046-0.27231.78190.00910.25980.3554-0.4953-0.0435-0.0983-0.30550.19090.00020.48690.0407-0.02360.54520.04360.44512.742814.475320.8418
130.2196-0.31770.33090.2989-0.31660.2704-0.31261.0373-0.5045-0.4863-0.1607-1.21030.4937-0.5538-0.01030.75540.02170.09250.6142-0.17460.4732-2.9073-3.881115.766
142.84820.73580.80531.3549-0.23822.9904-0.0879-0.1612-0.0211-0.48290.15120.3601-0.0197-0.10330.00020.3910.0192-0.01720.4322-0.00170.3554-6.4695.732123.7323
152.02230.8096-0.00880.5486-0.55222.5638-0.07560.10060.23530.28510.0159-0.5289-0.01180.4761-0.00010.37140.0158-0.03730.54580.03070.45464.108411.114529.6882
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 160 )
6X-RAY DIFFRACTION6chain 'A' and (resid 161 through 182 )
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 110 )
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 130 )
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 137 )
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 160 )
11X-RAY DIFFRACTION11chain 'B' and (resid 161 through 182 )
12X-RAY DIFFRACTION12chain 'C' and (resid 76 through 99 )
13X-RAY DIFFRACTION13chain 'C' and (resid 100 through 110 )
14X-RAY DIFFRACTION14chain 'C' and (resid 111 through 160 )
15X-RAY DIFFRACTION15chain 'C' and (resid 161 through 182 )

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