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- PDB-8b5i: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-1,3-dimet... -

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Basic information

Entry
Database: PDB / ID: 8b5i
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-1,3-dimethyl-1,3-dihydro-2H-benzo[d]azepin-2-one
ComponentsBromodomain-containing protein 2BRD2
KeywordsTRANSCRIPTION / INHIBITOR COMPLEX BROMODOMAIN
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...chromatin looping / acetylation-dependent protein binding / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-P0U / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsChung, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Identification and Optimization of a Ligand-Efficient Benzoazepinone Bromodomain and Extra Terminal (BET) Family Acetyl-Lysine Mimetic into the Oral Candidate Quality Molecule I-BET432.
Authors: Humphreys, P.G. / Anderson, N.A. / Bamborough, P. / Baxter, A. / Chung, C.W. / Cookson, R. / Craggs, P.D. / Dalton, T. / Fournier, J.C.L. / Gordon, L.J. / Gray, H.F. / Gray, M.W. / Gregory, ...Authors: Humphreys, P.G. / Anderson, N.A. / Bamborough, P. / Baxter, A. / Chung, C.W. / Cookson, R. / Craggs, P.D. / Dalton, T. / Fournier, J.C.L. / Gordon, L.J. / Gray, H.F. / Gray, M.W. / Gregory, R. / Hirst, D.J. / Jamieson, C. / Jones, K.L. / Kessedjian, H. / Lugo, D. / McGonagle, G. / Patel, V.K. / Patten, C. / Poole, D.L. / Prinjha, R.K. / Ramirez-Molina, C. / Rioja, I. / Seal, G. / Stafford, K.A.J. / Shah, R.R. / Tape, D. / Theodoulou, N.H. / Tomlinson, L. / Ukuser, S. / Wall, I.D. / Wellaway, N. / White, G.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2827
Polymers13,4321
Non-polymers8506
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.793, 52.400, 31.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-787-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13432.462 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Chemical ChemComp-P0U / (1~{R})-7,8-dimethoxy-1,3-dimethyl-1~{H}-3-benzazepin-2-one


Mass: 247.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 300, 0.1M MES buffer pH6.5

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Data collection

DiffractionMean temperature: 199 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→31.992 Å / Num. obs: 15915 / % possible obs: 96.9 % / Redundancy: 2.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.018 / Net I/σ(I): 35.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 9.6 / Num. unique obs: 1969 / CC1/2: 0.801 / % possible all: 83.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in hosue

Resolution: 1.604→31.992 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.651 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 761 4.81 %
Rwork0.1465 15059 -
all0.148 --
obs-15820 96.205 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 16.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.112 Å20 Å20 Å2
2--0.187 Å2-0 Å2
3----0.075 Å2
Refinement stepCycle: LAST / Resolution: 1.604→31.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 58 222 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131037
X-RAY DIFFRACTIONr_bond_other_d0.0010.016990
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.6581385
X-RAY DIFFRACTIONr_angle_other_deg1.3231.6162292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6675119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.20121.75457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.61515180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.021157
X-RAY DIFFRACTIONr_chiral_restr0.0680.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02234
X-RAY DIFFRACTIONr_nbd_refined0.2070.2216
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.2834
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2490
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2138
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.29
X-RAY DIFFRACTIONr_nbd_other0.1360.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0850.233
X-RAY DIFFRACTIONr_mcbond_it0.7261.493464
X-RAY DIFFRACTIONr_mcbond_other0.7171.486463
X-RAY DIFFRACTIONr_mcangle_it1.2623.341584
X-RAY DIFFRACTIONr_mcangle_other1.2633.352585
X-RAY DIFFRACTIONr_scbond_it1.2741.879573
X-RAY DIFFRACTIONr_scbond_other1.2731.88574
X-RAY DIFFRACTIONr_scangle_it2.1413.955800
X-RAY DIFFRACTIONr_scangle_other2.143.957801
X-RAY DIFFRACTIONr_lrange_it5.24416.3951276
X-RAY DIFFRACTIONr_lrange_other5.24316.4031277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.604-1.6450.24430.191841X-RAY DIFFRACTION75.0424
1.645-1.690.241550.1741026X-RAY DIFFRACTION91.3779
1.69-1.7390.216470.1611047X-RAY DIFFRACTION98.5586
1.739-1.7930.185650.1561036X-RAY DIFFRACTION99.2786
1.793-1.8510.144400.1391009X-RAY DIFFRACTION99.3371
1.851-1.9160.15420.143992X-RAY DIFFRACTION99.3276
1.916-1.9880.174420.139948X-RAY DIFFRACTION99.4975
1.988-2.0690.151410.135917X-RAY DIFFRACTION99.5842
2.069-2.1610.165360.129878X-RAY DIFFRACTION99.1323
2.161-2.2660.19440.131840X-RAY DIFFRACTION98.9922
2.266-2.3880.17300.132798X-RAY DIFFRACTION98.4542
2.388-2.5330.174440.139769X-RAY DIFFRACTION99.2674
2.533-2.7070.145450.135692X-RAY DIFFRACTION97.8752
2.707-2.9230.182340.14680X-RAY DIFFRACTION98.892
2.923-3.20.215320.153611X-RAY DIFFRACTION98.318
3.2-3.5750.189370.142549X-RAY DIFFRACTION97.5042
3.575-4.1240.148320.14484X-RAY DIFFRACTION96.8105
4.124-5.0380.191200.147418X-RAY DIFFRACTION95.0108
5.038-7.0750.185230.188332X-RAY DIFFRACTION95.1743
7.075-31.9920.22190.213192X-RAY DIFFRACTION84.4538
Refinement TLS params.Method: refined / Origin x: 32.765 Å / Origin y: 9.9562 Å / Origin z: 0.5968 Å
111213212223313233
T0.0018 Å2-0 Å20.0024 Å2-0.0014 Å2-0.0013 Å2--0.021 Å2
L0.9043 °20.051 °20.1837 °2-0.2872 °20.0346 °2--0.06 °2
S0.0316 Å °0.022 Å °0.0142 Å °0.0143 Å °-0.0137 Å °0.0028 Å °0.0057 Å °0.0047 Å °-0.0179 Å °
Refinement TLS groupSelection: ALL

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