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- PDB-6zb1: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK620 -

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Basic information

Entry
Database: PDB / ID: 6zb1
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH GSK620
ComponentsBromodomain-containing protein 2
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD2 / BROMODOMAIN CONTAINING PROTEIN 2 / ANTAGONIST
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 / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...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 / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / 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
Chem-QCZ / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2020
Title: The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor.
Authors: Seal, J.T. / Atkinson, S.J. / Aylott, H. / Bamborough, P. / Chung, C.W. / Copley, R.C.B. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Lindon, M. / Messenger, C. ...Authors: Seal, J.T. / Atkinson, S.J. / Aylott, H. / Bamborough, P. / Chung, C.W. / Copley, R.C.B. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Lindon, M. / Messenger, C. / Michon, A.M. / Mitchell, D. / Preston, A. / Prinjha, R.K. / Rioja, I. / Taylor, S. / Wall, I.D. / Watson, R.J. / Woolven, J.M. / Demont, E.H.
History
DepositionJun 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)13,8824
Polymers13,4321
Non-polymers4493
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint4 kcal/mol
Surface area6730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.428, 71.855, 31.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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-QCZ / ~{N}5-cyclopropyl-~{N}3-methyl-2-oxidanylidene-1-(phenylmethyl)pyridine-3,5-dicarboxamide


Mass: 325.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19N3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 45.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / 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: Oct 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→71.86 Å / Num. obs: 1588 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.017 / Net I/σ(I): 42
Reflection shellResolution: 1.6→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 12.3 / Num. unique obs: 1950 / % possible all: 83.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: in house structure

Resolution: 1.6→35.953 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.554 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.086
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1852 805 5.082 %
Rwork0.154 15036 -
all0.156 --
obs-15841 94.999 %
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: 12.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0 Å2
2---0.142 Å20 Å2
3---0.332 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms919 0 32 199 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131010
X-RAY DIFFRACTIONr_bond_other_d0.0010.017931
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.651360
X-RAY DIFFRACTIONr_angle_other_deg1.3491.6222159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8375117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94621.20758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77315177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.347158
X-RAY DIFFRACTIONr_chiral_restr0.0660.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02231
X-RAY DIFFRACTIONr_nbd_refined0.2160.2229
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.2789
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2483
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2810.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.28
X-RAY DIFFRACTIONr_nbd_other0.1780.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.220
X-RAY DIFFRACTIONr_mcbond_it0.8281.29462
X-RAY DIFFRACTIONr_mcbond_other0.8111.283461
X-RAY DIFFRACTIONr_mcangle_it1.4332.879581
X-RAY DIFFRACTIONr_mcangle_other1.4352.889582
X-RAY DIFFRACTIONr_scbond_it0.9021.443548
X-RAY DIFFRACTIONr_scbond_other0.9011.444549
X-RAY DIFFRACTIONr_scangle_it1.5623.132776
X-RAY DIFFRACTIONr_scangle_other1.5613.133777
X-RAY DIFFRACTIONr_lrange_it5.22413.4211267
X-RAY DIFFRACTIONr_lrange_other5.22213.4261268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6380.204400.184861X-RAY DIFFRACTION75.3344
1.638-1.6830.189470.1671001X-RAY DIFFRACTION88.4388
1.683-1.7320.203650.155978X-RAY DIFFRACTION93.2082
1.732-1.7850.222490.1571030X-RAY DIFFRACTION95.9111
1.785-1.8430.2520.154996X-RAY DIFFRACTION96.4121
1.843-1.9080.185470.156964X-RAY DIFFRACTION96.8391
1.908-1.980.157520.148944X-RAY DIFFRACTION97.3607
1.98-2.060.141520.14897X-RAY DIFFRACTION97.5334
2.06-2.1520.198470.144885X-RAY DIFFRACTION98.1053
2.152-2.2560.141380.139833X-RAY DIFFRACTION97.3184
2.256-2.3780.176490.143803X-RAY DIFFRACTION98.9547
2.378-2.5220.183430.149742X-RAY DIFFRACTION97.8803
2.522-2.6950.195500.144727X-RAY DIFFRACTION98.4791
2.695-2.910.198390.148680X-RAY DIFFRACTION98.8996
2.91-3.1870.187320.162623X-RAY DIFFRACTION99.0923
3.187-3.560.209280.142580X-RAY DIFFRACTION99.1843
3.56-4.1060.166220.157515X-RAY DIFFRACTION98.5321
4.106-5.0170.172240.161429X-RAY DIFFRACTION97.8402
5.017-7.0460.237200.194346X-RAY DIFFRACTION97.6
7.046-35.9530.22590.212202X-RAY DIFFRACTION87.1901
Refinement TLS params.Method: refined / Origin x: 10.2825 Å / Origin y: 3.0094 Å / Origin z: 0.8936 Å
111213212223313233
T0.0018 Å2-0.0013 Å20.0017 Å2-0.0033 Å2-0.0027 Å2--0.0036 Å2
L0.339 °2-0.2651 °20.0493 °2-0.9052 °2-0.1555 °2--0.1542 °2
S-0.0094 Å °-0.0168 Å °-0.0026 Å °-0.0194 Å °0.0304 Å °-0.0032 Å °-0.0053 Å °0.011 Å °-0.0209 Å °
Refinement TLS groupSelection: ALL

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