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- PDB-2yek: Crystal Structure of the First Bromodomain of Human Brd2 with the... -

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Basic information

Entry
Database: PDB / ID: 2yek
TitleCrystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GSK525762 (IBET)
ComponentsBROMODOMAIN-CONTAINING PROTEIN 2BRD2
KeywordsSIGNALING PROTEIN / HISTONE / EPIGENETIC READER
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-EAM / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsChung, C.W.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Discovery and Characterization of Small Molecule Inhibitors of the Bet Family Bromodomains.
Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / ...Authors: Chung, C.W. / Coste, H. / White, J.H. / Mirguet, O. / Wilde, J. / Gosmini, R.L. / Delves, C. / Magny, S.M. / Woodward, R. / Hughes, S.A. / Boursier, E.V. / Flynn, H. / Bouillot, A.M. / Bamborough, P. / Brusq, J.M. / Gellibert, F.J. / Jones, E.J. / Riou, A.M. / Homes, P. / Martin, S.L. / Uings, I.J. / Toum, J. / Clement, C.A. / Boullay, A.B. / Grimley, R.L. / Blandel, F.M. / Prinjha, R.K. / Lee, K. / Kirilovsky, J. / Nicodeme, E.
History
DepositionMar 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references / Version format compliance
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
B: BROMODOMAIN-CONTAINING PROTEIN 2
C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7067
Polymers53,3393
Non-polymers1,3684
Water7,152397
1
A: BROMODOMAIN-CONTAINING PROTEIN 2
B: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4074
Polymers35,5592
Non-polymers8482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-11.9 kcal/mol
Surface area11300 Å2
MethodPISA
2
C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules

C: BROMODOMAIN-CONTAINING PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5996
Polymers35,5592
Non-polymers1,0404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2360 Å2
ΔGint-36 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.243, 55.639, 66.231
Angle α, β, γ (deg.)90.00, 93.63, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-2092-

HOH

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Components

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


Mass: 17779.547 Da / Num. of mol.: 3 / 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-EAM / 2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide


Mass: 423.895 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H22ClN5O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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 Å3/Da / Density % sol: 38.61 % / Description: NONE
Crystal growpH: 7 / Details: 26% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M HEPES PH 7.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.98→25.96 Å / Num. obs: 28832 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→25.96 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.864 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20079 1461 5.1 %RANDOM
Rwork0.15546 ---
obs0.15773 27369 100 %-
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: 32.555 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å2-0.91 Å2
2---0.32 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.98→25.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2738 0 95 397 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223036
X-RAY DIFFRACTIONr_bond_other_d0.0010.022007
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.9614136
X-RAY DIFFRACTIONr_angle_other_deg0.81734926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6025350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6725142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5981510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213450
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
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_it0.9321722
X-RAY DIFFRACTIONr_mcbond_other0.1552665
X-RAY DIFFRACTIONr_mcangle_it1.72742823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28841314
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.46661313
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: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 114 -
Rwork0.199 1970 -
obs--100 %
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)
11.2499-0.1095-0.20660.4887-0.06911.1263-0.0533-0.024-0.0719-0.0053-0.00140.1126-0.0143-0.06460.05470.02350.01030.00960.0105-0.00670.05416.73036.23552.3217
21.0952-0.01010.43380.77370.18551.46030.0267-0.0976-0.02040.04860.0277-0.0468-0.0209-0.0019-0.05450.0363-0.0055-0.00520.01370.00950.036935.80568.586910.1648
30.8857-0.30540.74041.5369-0.37041.7466-0.03510.0676-0.0572-0.11410.0905-0.0059-0.12060.1113-0.05540.0245-0.0070.00930.08010.00840.0095-1.856619.078522.6004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A74 - 187
2X-RAY DIFFRACTION2B76 - 182
3X-RAY DIFFRACTION3C76 - 181

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