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- PDB-7nq9: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 2-benzyl-N-cyclopropyl-... -

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Basic information

Entry
Database: PDB / ID: 7nq9
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 2-benzyl-N-cyclopropyl-6-(1-methyl-1H-1,2,3-triazol-4-yl)isonicotinamide
ComponentsBromodomain-containing protein 2
KeywordsNUCLEAR PROTEIN / 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 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
Chem-UMB / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.602 Å
AuthorsChung, C.W.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Template-Hopping Approach Leads to Potent, Selective, and Highly Soluble Bromo and Extraterminal Domain (BET) Second Bromodomain (BD2) Inhibitors.
Authors: Aylott, H.E. / Atkinson, S.J. / Bamborough, P. / Bassil, A. / Chung, C.W. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Messenger, C. / Mitchell, D. / Phillipou, ...Authors: Aylott, H.E. / Atkinson, S.J. / Bamborough, P. / Bassil, A. / Chung, C.W. / Gordon, L. / Grandi, P. / Gray, J.R.J. / Harrison, L.A. / Hayhow, T.G. / Messenger, C. / Mitchell, D. / Phillipou, A. / Preston, A. / Prinjha, R.K. / Rianjongdee, F. / Rioja, I. / Seal, J.T. / Wall, I.D. / Watson, R.J. / Woolven, J.M. / Demont, E.H.
History
DepositionMar 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: 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 1.2Jun 19, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
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)14,0827
Polymers13,4321
Non-polymers6506
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint12 kcal/mol
Surface area6670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.759, 52.443, 32.070
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-747-

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-UMB / 6-benzyl-N4-((1r,3r)-3-hydroxycyclobutyl)-N2-methylpyridine-2,4-dicarboxamide / ~{N}2-methyl-~{N}4-(3-oxidanylcyclobutyl)-6-(phenylmethyl)pyridine-2,4-dicarboxamide


Mass: 339.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.6→72.02 Å / Num. obs: 15827 / % possible obs: 95.4 % / Redundancy: 2.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.023 / Net I/σ(I): 25.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1868 / CC1/2: 0.817 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.602→29.279 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.467 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1783 784 4.963 %
Rwork0.1528 15013 -
all0.154 --
obs-15797 95.571 %
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: 18.151 Å2
Baniso -1Baniso -2Baniso -3
1--0.466 Å2-0 Å2-0 Å2
2---0.183 Å20 Å2
3---0.649 Å2
Refinement stepCycle: LAST / Resolution: 1.602→29.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 45 170 1125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131026
X-RAY DIFFRACTIONr_bond_other_d0.0010.017945
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.651379
X-RAY DIFFRACTIONr_angle_other_deg1.2531.6222194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6435119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34521.35659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16715178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.217158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021219
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02233
X-RAY DIFFRACTIONr_nbd_refined0.1980.2219
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1630.2786
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2485
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2122
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.27
X-RAY DIFFRACTIONr_nbd_other0.1690.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1090.221
X-RAY DIFFRACTIONr_mcbond_it1.1792.064465
X-RAY DIFFRACTIONr_mcbond_other1.1282.051463
X-RAY DIFFRACTIONr_mcangle_it2.0294.609588
X-RAY DIFFRACTIONr_mcangle_other2.044.629588
X-RAY DIFFRACTIONr_scbond_it1.6742.472561
X-RAY DIFFRACTIONr_scbond_other1.6722.472562
X-RAY DIFFRACTIONr_scangle_it2.8295.293789
X-RAY DIFFRACTIONr_scangle_other2.8275.295790
X-RAY DIFFRACTIONr_lrange_it5.67720.8141243
X-RAY DIFFRACTIONr_lrange_other5.42319.3251194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.602-1.6440.249400.2158720.21711880.9060.9176.76770.176
1.644-1.6890.228530.2089520.20911910.9240.91684.38290.163
1.689-1.7370.191700.1879920.18711040.9180.92496.19560.153
1.737-1.7910.187540.18110250.18211130.9280.94396.94520.144
1.791-1.8490.212410.1610020.16210690.9430.96297.56780.132
1.849-1.9140.191590.1589340.1610200.9570.96197.35290.128
1.914-1.9860.23270.159810.15110200.9450.96598.82350.126
1.986-2.0660.212530.1479070.159720.9510.96798.76540.126
2.066-2.1580.18480.1438720.1459230.9660.97199.6750.124
2.158-2.2630.154420.1378460.1378940.9640.97499.32890.117
2.263-2.3840.14480.1338010.1348570.9760.97699.06650.113
2.384-2.5280.202360.1347460.1377870.9580.97599.36470.118
2.528-2.7010.14370.1367300.1367740.970.97599.09560.121
2.701-2.9150.177440.1436760.1457280.9650.97498.90110.134
2.915-3.190.173380.1516070.1526520.9680.97398.92640.139
3.19-3.5610.141230.1335830.1336140.9750.9898.69710.128
3.561-4.1020.147300.1415070.1415410.9750.98299.26060.147
4.102-50.212160.1564340.1584570.9670.97998.46830.166
5-6.970.185140.1883500.1883780.9760.96596.29630.194
6.97-29.2790.211110.2021960.2032430.9540.96385.18520.205

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