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- PDB-4a9n: N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-cyclopropyl-5-(3,5- d... -

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Basic information

Entry
Database: PDB / ID: 4a9n
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-cyclopropyl-5-(3,5- dimethyl-1,2-oxazol-4-yl)-2-methylbenzene-1-sulfonamide
ComponentsBROMODOMAIN CONTAINING 2
KeywordsSIGNALING PROTEIN/INHIBITOR / SIGNALING PROTEIN-INHIBITOR COMPLEX
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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-A9N / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChung, C. / Bamborough, P.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Fragment-Based Discovery of Bromodomain Inhibitors Part 2: Optimization of Phenylisoxazole Sulfonamides.
Authors: Bamborough, P. / Diallo, H. / Goodacre, J.D. / Gordon, L. / Lewis, A. / Seal, J.T. / Wilson, D.M. / Woodrow, M.D. / Chung, C.W.
History
DepositionNov 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BROMODOMAIN CONTAINING 2
B: BROMODOMAIN CONTAINING 2
C: BROMODOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,17016
Polymers53,7263
Non-polymers1,44413
Water5,062281
1
A: BROMODOMAIN CONTAINING 2
B: BROMODOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,02512
Polymers35,8172
Non-polymers1,20710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-30.2 kcal/mol
Surface area11840 Å2
MethodPISA
2
C: BROMODOMAIN CONTAINING 2
hetero molecules

C: BROMODOMAIN CONTAINING 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2908
Polymers35,8172
Non-polymers4736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3480 Å2
ΔGint-26.7 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.967, 55.725, 68.126
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2052-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein BROMODOMAIN CONTAINING 2 / HUMAN BRD2


Mass: 17908.727 Da / Num. of mol.: 3 / Fragment: N-TERMINAL BROMODOMAIN (BD1), RESIDUES 67-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25440

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Non-polymers , 5 types, 294 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-A9N / N-CYCLOPROP-2-EN-1-YL-5-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-2-METHYL-BENZENESULFONAMIDE


Mass: 304.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16N2O3S
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.67 % / Description: NONE
Crystal growTemperature: 293 K / pH: 7
Details: 0.1 M HEPES PH 7.0, 22-28% PEG 3350, 0.2 M (NH4)2SO4, 20 DEGREES CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.072
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2009
RadiationMonochromator: 1.072 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.86→67.88 Å / Num. obs: 35351 / % possible obs: 97.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 86

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→67.88 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.09 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19507 1405 4 %RANDOM
Rwork0.17383 ---
obs0.1747 33945 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.975 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å2-1.78 Å2
2---1.6 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.85→67.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2774 0 90 281 3145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222989
X-RAY DIFFRACTIONr_bond_other_d0.0010.022038
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9574049
X-RAY DIFFRACTIONr_angle_other_deg0.76834981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1035342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.94924.965141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06715534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1741510
X-RAY DIFFRACTIONr_chiral_restr0.050.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.63121711
X-RAY DIFFRACTIONr_mcbond_other0.0912666
X-RAY DIFFRACTIONr_mcangle_it1.22242790
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.45741278
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.40361253
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.855→1.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 97 -
Rwork0.304 2137 -
obs--83.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6354-0.7734-0.02552.52740.4381.9941-0.083-0.0408-0.07780.162-0.02520.38530.0311-0.18210.10820.0210.00520.04580.040.00310.110116.24286.80421.7371
21.3366-0.51080.0062.690.10412.2997-0.0226-0.12410.01450.31410.089-0.107-0.09230.0944-0.06650.05810.0051-0.01460.02120.00610.03934.36019.214711.176
31.5855-0.08321.36823.4304-1.56275.7756-0.03640.13490.008-0.28560.0772-0.0925-0.0140.0797-0.04080.03010.00570.01080.1347-0.00190.0133-2.078918.823723.6294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A75 - 186
2X-RAY DIFFRACTION2B72 - 186
3X-RAY DIFFRACTION3C77 - 182

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