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- PDB-4alg: N-Terminal Bromodomain of Human BRD2 With IBET-151 -

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Basic information

Entry
Database: PDB / ID: 4alg
TitleN-Terminal Bromodomain of Human BRD2 With IBET-151
ComponentsBROMODOMAIN-CONTAINING PROTEIN 2
KeywordsSIGNALING PROTEIN / INHIBITOR / HISTONE / EPIGENETIC READER
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / 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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1GH / ACETATE ION / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChung, C. / Lamotte, Y. / Donche, F. / Bouillot, A. / Mirguet, O.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Identification of a Novel Series of Bet Family Bromodomain Inhibitors: Binding Mode and Profile of I-Bet151 (Gsk1210151A).
Authors: Seal, J. / Lamotte, Y. / Donche, F. / Bouillot, A. / Mirguet, O. / Gellibert, F. / Nicodeme, E. / Krysa, G. / Kirilovsky, J. / Beinke, S. / Mccleary, S. / Rioja, I. / Bamborough, P. / Chung, ...Authors: Seal, J. / Lamotte, Y. / Donche, F. / Bouillot, A. / Mirguet, O. / Gellibert, F. / Nicodeme, E. / Krysa, G. / Kirilovsky, J. / Beinke, S. / Mccleary, S. / Rioja, I. / Bamborough, P. / Chung, C. / Gordon, L. / Lewis, T. / Walker, A.L. / Cutler, L. / Lugo, D. / Wilson, D.M. / Witherington, J. / Lee, K. / Prinjha, R.K.
History
DepositionMar 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 15, 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 PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4754
Polymers17,9091
Non-polymers5673
Water2,288127
1
A: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules

A: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9518
Polymers35,8172
Non-polymers1,1336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2760 Å2
ΔGint-13.6 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.050, 40.303, 48.347
Angle α, β, γ (deg.)90.00, 113.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 2 / BRD2 / O27.1.1 / REALLY INTERESTING NEW GENE 3 PROTEIN


Mass: 17908.727 Da / Num. of mol.: 1 / Fragment: N-TERMINAL BROMODOMAIN, 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
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1GH / 7-(3,5-DIMETHYL-1,2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H,2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE


Mass: 415.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H21N5O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details7-(3,5-DIMETHYL-1, 2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H, 2H,3H-IMIDAZO[4,5-C] ...7-(3,5-DIMETHYL-1, 2-OXAZOL-4-YL)-8-METHOXY-1-[(1R)-1-(PYRIDIN-2-YL)ETHYL]-1H, 2H,3H-IMIDAZO[4,5-C]QUINOLIN-2-ONE (LIG): REFERRED TO IBET-151
Sequence detailsCRYSTALLISATION PROTEIN USED CONTAINS N-TERMINAL HIS6 TAG.

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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: 2.05 Å3/Da / Density % sol: 40.03 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.7 / Details: 150MM NH4SO4, 25%MME, 100MM NAAC PH 4.7, 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.6→44.41 Å / Num. obs: 18099 / % possible obs: 93.8 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.41 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.956 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20214 914 5.1 %RANDOM
Rwork0.17566 ---
obs0.17701 17180 93.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å22.78 Å2
2--0.67 Å20 Å2
3---1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 41 127 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191069
X-RAY DIFFRACTIONr_bond_other_d0.0010.02724
X-RAY DIFFRACTIONr_angle_refined_deg0.9841.9421451
X-RAY DIFFRACTIONr_angle_other_deg0.79731767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5655121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7182550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79715190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.214154
X-RAY DIFFRACTIONr_chiral_restr0.0590.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02211
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 40 -
Rwork0.311 883 -
obs--66.16 %
Refinement TLS params.Method: refined / Origin x: 24.6715 Å / Origin y: 0.6716 Å / Origin z: 14.8435 Å
111213212223313233
T0.065 Å2-0.0134 Å2-0.0148 Å2-0.0563 Å2-0.0096 Å2--0.0434 Å2
L2.616 °20.119 °2-1.0423 °2-0.3223 °2-0.0784 °2--0.5838 °2
S0.0654 Å °0.162 Å °0.0076 Å °-0.0261 Å °0.0054 Å °0.0525 Å °-0.0602 Å °-0.0131 Å °-0.0708 Å °

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