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- PDB-7nq2: C-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-N4-cyclopropyl-N2-m... -

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Basic information

Entry
Database: PDB / ID: 7nq2
TitleC-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH (S)-N4-cyclopropyl-N2-methyl-6-(1-phenylethyl)pyridine-2,4-dicarboxamide
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-ULE / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.735 Å
AuthorsChung, C.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Identification of a Series of N -Methylpyridine-2-carboxamides as Potent and Selective Inhibitors of the Second Bromodomain (BD2) of the Bromo and Extra Terminal Domain (BET) Proteins.
Authors: Harrison, L.A. / Atkinson, S.J. / Bassil, A. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Levernier, E. / Lewis, A. / Lugo, D. / Messenger, C. / Michon, A.M. / Mitchell, D.J. / Preston, A. / ...Authors: Harrison, L.A. / Atkinson, S.J. / Bassil, A. / Chung, C.W. / Grandi, P. / Gray, J.R.J. / Levernier, E. / Lewis, A. / Lugo, D. / Messenger, C. / Michon, A.M. / Mitchell, D.J. / Preston, A. / Prinjha, R.K. / Rioja, I. / Seal, J.T. / Taylor, S. / Wall, I.D. / Watson, R.J. / Woolven, J.M. / Demont, E.H.
History
DepositionFeb 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)13,8804
Polymers13,4321
Non-polymers4483
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint3 kcal/mol
Surface area6870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.889, 52.382, 32.114
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-ULE / ~{N}4-cyclopropyl-~{N}2-methyl-6-[(1~{S})-1-phenylethyl]pyridine-2,4-dicarboxamide


Mass: 323.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 45.35 %
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: Jan 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→32.11 Å / Num. obs: 12927 / % possible obs: 98.5 % / Redundancy: 2.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.2
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1842 / CC1/2: 0.792 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.735→29.638 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.265 / SU ML: 0.071 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.104
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1944 659 5.111 %
Rwork0.1614 12236 -
all0.163 --
obs-12895 98.195 %
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: 19.004 Å2
Baniso -1Baniso -2Baniso -3
1--0.492 Å2-0 Å2-0 Å2
2---0.071 Å20 Å2
3---0.564 Å2
Refinement stepCycle: LAST / Resolution: 1.735→29.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 32 148 1103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.013996
X-RAY DIFFRACTIONr_bond_other_d0.0010.017913
X-RAY DIFFRACTIONr_angle_refined_deg1.2181.641341
X-RAY DIFFRACTIONr_angle_other_deg1.2461.6242123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.285115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81922.32156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19515174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.606156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02218
X-RAY DIFFRACTIONr_nbd_refined0.20.2206
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.2783
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2471
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.26
X-RAY DIFFRACTIONr_nbd_other0.1430.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.221
X-RAY DIFFRACTIONr_mcbond_it1.7392.282455
X-RAY DIFFRACTIONr_mcbond_other1.6132.269453
X-RAY DIFFRACTIONr_mcangle_it3.0255.079569
X-RAY DIFFRACTIONr_mcangle_other3.0415.098569
X-RAY DIFFRACTIONr_scbond_it1.9432.58541
X-RAY DIFFRACTIONr_scbond_other1.9422.581542
X-RAY DIFFRACTIONr_scangle_it3.3315.546768
X-RAY DIFFRACTIONr_scangle_other3.3285.549769
X-RAY DIFFRACTIONr_lrange_it6.39821.5351197
X-RAY DIFFRACTIONr_lrange_other6.06420.5171154
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
1.735-1.780.304510.2468870.2499610.8730.87897.60670.217
1.78-1.8280.201430.2268490.2249010.9310.90599.00110.187
1.828-1.8810.266550.2068520.219110.910.91899.56090.175
1.881-1.9390.207470.1948180.1948730.920.93399.08360.159
1.939-2.0020.184470.1767950.1768510.9560.94298.94240.146
2.002-2.0720.238440.1737700.1778200.9370.94699.26830.145
2.072-2.150.211390.1587600.168080.9520.95798.88610.131
2.15-2.2370.153340.1517020.1517470.9670.96498.52740.121
2.237-2.3360.233340.146990.1447460.9480.96798.25740.113
2.336-2.4490.19330.1546630.1567090.9490.96398.16640.123
2.449-2.5810.169290.1396300.146640.9580.96999.2470.115
2.581-2.7360.151340.1586070.1576510.9710.96798.46390.127
2.736-2.9230.224370.1435720.1486170.9510.97298.70340.12
2.923-3.1550.179190.1385250.145530.9720.97498.37250.113
3.155-3.4520.149300.1414990.1425350.9780.97898.87850.121
3.452-3.8530.193230.1414440.1434810.9540.98197.08940.131
3.853-4.4370.186220.1443930.1464300.9750.97796.51160.137
4.437-5.4040.186190.1633350.1653690.9720.97495.9350.16
5.404-7.5180.156100.2052750.2033070.9720.96192.83390.191
7.518-29.6380.16590.181610.1791950.9540.96587.17950.191

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