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

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Basic information

Entry
Database: PDB / ID: 7vro
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


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / histone reader activity / : / neural tube closure / nucleosome assembly / spermatogenesis ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / histone reader activity / : / 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 / Bromodomain (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
THEOBROMINE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 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 23, 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)45,76111
Polymers44,6563
Non-polymers1,1058
Water3,783210
1
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6959
Polymers29,7712
Non-polymers9257
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-47 kcal/mol
Surface area11560 Å2
MethodPISA
2
C: Bromodomain-containing protein 2
hetero molecules

C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1314
Polymers29,7712
Non-polymers3602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area3260 Å2
ΔGint-38 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.129, 55.489, 67.659
Angle α, β, γ (deg.)90.00, 93.88, 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25440
#2: Chemical
ChemComp-37T / THEOBROMINE / 3,7-DIMETHYLXANTHINE / 3,7-DIMETHYLPURINE-2,6-DIONE


Mass: 180.164 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
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 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.35→31.33 Å / Num. obs: 17885 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC1/2: 1 / Rmerge(I) obs: 0.107 / Net I/σ(I): 19.63
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.291 / Num. unique obs: 833 / CC1/2: 0.96 / % possible all: 93.6

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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: 2.35→31.33 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 880 4.97 %
Rwork0.174 --
obs0.1768 17695 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→31.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 72 210 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082824
X-RAY DIFFRACTIONf_angle_d0.8093838
X-RAY DIFFRACTIONf_dihedral_angle_d4.595387
X-RAY DIFFRACTIONf_chiral_restr0.045397
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.50.24531410.1872717X-RAY DIFFRACTION97
2.5-2.690.2721410.19822773X-RAY DIFFRACTION100
2.69-2.960.24541510.19672809X-RAY DIFFRACTION100
2.96-3.390.28071460.19132812X-RAY DIFFRACTION100
3.39-4.270.19931500.15182832X-RAY DIFFRACTION100
4.27-31.330.21591510.16522872X-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)
12.28371.3581-0.15080.8922-0.5753.1503-0.06050.07280.19020.0460.1207-0.0011-0.27580.26210.00090.29270.03350.0070.45170.00270.2845-0.563722.299697.52
21.1274-0.25690.37670.59510.25230.46520.2361-0.4521-0.21840.3714-0.15060.9049-0.08650.2155-0.00030.35360.01640.12990.35970.0590.48615.239910.390675.9171
30.20280.22650.01470.22010.01160.32530.26930.8538-0.1443-0.6761-0.7340.5317-0.2244-0.0973-0.00140.37750.0626-0.04890.5437-0.04530.438311.63347.354155.5985
43.2956-1.61170.96372.61181.16182.2035-0.1221-0.2673-0.29370.1001-0.05520.41130.1536-0.2033-0.00020.29130.00430.00730.26560.00050.409613.49722.678567.2918
51.8867-0.13840.63291.02840.35120.4617-0.0987-0.2472-0.05730.46610.0563-0.0511-0.3390.0608-0.00380.39040.03710.01920.28090.03910.349915.427613.463674.215
60.881-0.28310.08090.3005-0.00820.03510.1266-0.98050.79781.3016-0.0747-0.20580.183-0.96660.00150.6706-0.0288-0.03330.6379-0.00860.299623.684210.277391.8531
70.1401-0.07260.07960.0417-0.04280.03180.15350.07210.23310.78690.264-0.23190.53570.7473-0.00220.50020.0549-0.04610.2959-0.04840.290530.12153.510185.7557
80.32220.16770.07810.0822-0.02440.0785-0.0271-0.18470.2534-0.5273-0.2783-0.46920.45470.69680.00060.33870.0193-0.07260.3374-0.00410.313135.1717-0.572977.8828
90.31110.34710.37440.93110.08061.04620.1380.01240.5-0.0247-0.1941-0.4455-0.44180.8851-0.00080.377-0.0368-0.0020.39140.02560.460338.526413.030169.5857
100.5227-0.0509-0.28640.5128-0.04560.4408-0.142-0.34170.18990.29210.3437-1.031-0.88890.58710.00920.5922-0.044-0.19260.40150.02330.352133.736613.92485.9335
111.7569-0.30430.52551.6342-1.04320.88160.0033-0.240.16150.38640.1794-0.1221-0.1368-0.20260.00080.38150.0128-0.02870.2937-0.0030.357226.576313.752377.9629
120.0538-0.0146-0.0260.0913-0.00420.01970.28580.3392-0.4204-0.5858-0.4249-0.3393-0.02550.62880.0010.36070.0320.04560.28890.00930.28831.93052.102661.5067
131.60750.22210.93611.8901-1.14241.3801-0.0146-0.0803-0.47260.3762-0.19530.28050.0129-0.5971-0.00140.34820.00830.02440.30870.02070.292723.44332.231278.5125
140.13960.08940.01240.0968-0.04830.0094-0.24340.67860.9096-0.2307-0.125-0.6598-1.2637-0.4196-0.00050.70470.0203-0.03430.50050.07810.4086-6.755334.245489.8745
150.17850.1687-0.10860.084-0.08910.1975-0.07010.3560.19-0.65550.0645-0.7019-0.00390.4246-0.00030.32770.00980.07280.4370.02580.39431.606620.57287.8529
160.3003-0.27360.01770.30410.11830.17660.1101-0.025-0.5609-0.3824-0.3727-0.72531.16270.46880.0010.8462-0.07450.12710.535-0.11220.4602-7.63366.076284.3504
171.7532-0.47211.0480.76740.06912.19310.0320.08870.0071-0.31550.06610.4141-0.1225-0.1672-0.00020.3591-0.0264-0.00660.48740.02090.3882-13.341619.496387.4205
181.66181.4302-0.15261.2469-0.40372.90030.0591-0.0982-0.0806-0.32940.06960.05390.0367-0.03980.00020.2733-0.00560.00730.4151-0.00640.278-7.974915.151195.8087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 161 through 182 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 182 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 84 )
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 99 )
9X-RAY DIFFRACTION9chain 'B' and (resid 100 through 122 )
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 132 )
11X-RAY DIFFRACTION11chain 'B' and (resid 133 through 155 )
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 160 )
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 182 )
14X-RAY DIFFRACTION14chain 'C' and (resid 76 through 84 )
15X-RAY DIFFRACTION15chain 'C' and (resid 85 through 99 )
16X-RAY DIFFRACTION16chain 'C' and (resid 100 through 112 )
17X-RAY DIFFRACTION17chain 'C' and (resid 113 through 137 )
18X-RAY DIFFRACTION18chain 'C' and (resid 138 through 160 )

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