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- PDB-8b5g: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-3-methyl-... -

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Basic information

Entry
Database: PDB / ID: 8b5g
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 7,8-dimethoxy-3-methyl-1,3-dihydro-2H-benzo[d]azepin-2-one
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / INHIBITOR COMPLEX BROMODOMAIN
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, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / 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
7,8-dimethoxy-3-methyl-1~{H}-3-benzazepin-2-one / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.619 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

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Assembly

Deposited unit
AAA: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9855
Polymers13,4321
Non-polymers5534
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area6820 Å2
Unit cell
Length a, b, c (Å)71.906, 52.421, 32.086
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-805-

HOH

21AAA-857-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / 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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-P4M / 7,8-dimethoxy-3-methyl-1~{H}-3-benzazepin-2-one / 7,8-dimethoxy-3-methyl-1,3-dihydro-2H-benzo[d]azepin-2-one


Mass: 233.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 300, 0.1M MES buffer pH6.5

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Data collection

DiffractionMean temperature: 100 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: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.619→71.39 Å / Num. obs: 15360 / % possible obs: 96.3 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.013 / Net I/σ(I): 52.1
Reflection shellResolution: 1.619→1.71 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.031 / Mean I/σ(I) obs: 22.2 / Num. unique obs: 1928 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: In house

Resolution: 1.619→21.808 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.552 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1827 758 4.971 %
Rwork0.1483 14490 -
all0.15 --
obs-15248 94.938 %
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: 13.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.094 Å20 Å2-0 Å2
2---0.051 Å20 Å2
3----0.043 Å2
Refinement stepCycle: LAST / Resolution: 1.619→21.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 37 260 1212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131024
X-RAY DIFFRACTIONr_bond_other_d0.0010.015959
X-RAY DIFFRACTIONr_angle_refined_deg1.231.6541382
X-RAY DIFFRACTIONr_angle_other_deg1.351.6182220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9395120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06121.75457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32215180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.736157
X-RAY DIFFRACTIONr_chiral_restr0.0680.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02238
X-RAY DIFFRACTIONr_nbd_refined0.2060.2234
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.2817
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2502
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2161
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.28
X-RAY DIFFRACTIONr_nbd_other0.130.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.242
X-RAY DIFFRACTIONr_mcbond_it0.6941.255468
X-RAY DIFFRACTIONr_mcbond_other0.6681.248467
X-RAY DIFFRACTIONr_mcangle_it1.2112.807592
X-RAY DIFFRACTIONr_mcangle_other1.2132.818593
X-RAY DIFFRACTIONr_scbond_it0.9851.491556
X-RAY DIFFRACTIONr_scbond_other0.9851.484554
X-RAY DIFFRACTIONr_scangle_it1.6633.231790
X-RAY DIFFRACTIONr_scangle_other1.6623.236791
X-RAY DIFFRACTIONr_lrange_it5.00514.6251322
X-RAY DIFFRACTIONr_lrange_other5.00314.6391323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.619-1.6610.187500.164843X-RAY DIFFRACTION76.1945
1.661-1.7060.234470.159976X-RAY DIFFRACTION92.4119
1.706-1.7560.184380.1451039X-RAY DIFFRACTION97.027
1.756-1.8090.176640.148967X-RAY DIFFRACTION97.9107
1.809-1.8680.224390.151994X-RAY DIFFRACTION98.9464
1.868-1.9330.206570.149944X-RAY DIFFRACTION98.913
1.933-2.0060.151440.14928X-RAY DIFFRACTION98.9817
2.006-2.0870.176490.135854X-RAY DIFFRACTION99.0132
2.087-2.1790.145500.138869X-RAY DIFFRACTION98.8172
2.179-2.2850.166480.131802X-RAY DIFFRACTION98.1524
2.285-2.4070.146370.13769X-RAY DIFFRACTION97.9344
2.407-2.5520.167350.148729X-RAY DIFFRACTION97.9487
2.552-2.7260.204330.147683X-RAY DIFFRACTION97.1506
2.726-2.9410.221400.159636X-RAY DIFFRACTION96.0227
2.941-3.2170.183400.152582X-RAY DIFFRACTION96.5838
3.217-3.590.195230.148537X-RAY DIFFRACTION94.7547
3.59-4.130.162180.141459X-RAY DIFFRACTION91.7308
4.13-5.0230.194220.154397X-RAY DIFFRACTION92.0879
5.023-6.9610.182150.193309X-RAY DIFFRACTION87.0968
6.961-21.6260.23390.195173X-RAY DIFFRACTION76.1506
Refinement TLS params.Method: refined / Origin x: 32.9867 Å / Origin y: 10.2494 Å / Origin z: 0.8053 Å
111213212223313233
T0.003 Å20.0003 Å20.0025 Å2-0.001 Å2-0.0008 Å2--0.0034 Å2
L0.9741 °20.1047 °20.211 °2-0.1724 °20.062 °2--0.1009 °2
S0.0151 Å °0.0032 Å °0.0115 Å °-0.0034 Å °-0.0084 Å °0.0002 Å °-0.0089 Å °-0.0017 Å °-0.0067 Å °
Refinement TLS groupSelection: ALL

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