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- PDB-5acy: N-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-(2R,4S)-2-methyl-4-(p... -

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Basic information

Entry
Database: PDB / ID: 5acy
TitleN-TERMINAL BROMODOMAIN OF HUMAN BRD4 WITH 1-(2R,4S)-2-methyl-4-(phenylamino)-6-4-(piperidin-1-ylmethyl)phenyl-1,2,3,4- tetrahydroquinolin-1-yl-ethan-1-one
ComponentsBROMODOMAIN-CONTAINING PROTEIN 4
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / BRD4 / BROMODOMAIN CONTAINING PROTEIN 4 / ANTAGONIST
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain-like ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-9S3 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsChung, C.
CitationJournal: J.Exp.Med. / Year: 2015
Title: Autism-Like Syndrome is Induced by Pharmacological Suppression of Bet Proteins in Young Mice.
Authors: Sullivan, J.M. / Badimon, A. / Schaefer, U. / Ayata, P. / Gray, J. / Chung, C. / Von Schimmelmann, M. / Zhang, F. / Garton, N. / Smithers, N. / Lewis, H. / Tarakhovsky, A. / Prinjha, R.K. / Schaefer, A.
History
DepositionAug 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
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 4
B: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2927
Polymers30,1992
Non-polymers1,0935
Water5,531307
1
A: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7395
Polymers15,0991
Non-polymers6404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BROMODOMAIN-CONTAINING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5532
Polymers15,0991
Non-polymers4541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.149, 59.497, 108.025
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BROMODOMAIN-CONTAINING PROTEIN 4 / PROTEIN HUNK1 / HUMAN BRD4


Mass: 15099.380 Da / Num. of mol.: 2 / Fragment: N-TERMINAL BROMODOMAIN, RESIDUES 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9S3 / 1-[(2S,4R)-2-methyl-4-(phenylamino)-6-[4-(piperidin-1-ylmethyl)phenyl]-3,4-dihydroquinolin-1(2H)-yl]ethanone


Mass: 453.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H35N3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.24 Å3/Da / Density % sol: 45.15 % / Description: NONE
Crystal growDetails: 0.1M MIB PH 4.0 25% PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.01→36.01 Å / Num. obs: 18016 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.1
Reflection shellResolution: 2.01→2.13 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.01→33.23 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.538 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27081 894 5 %RANDOM
Rwork0.21126 ---
obs0.21425 17095 96.03 %-
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: 29.857 Å2
Baniso -1Baniso -2Baniso -3
1--9.64 Å20 Å20 Å2
2--17.1 Å20 Å2
3----7.47 Å2
Refinement stepCycle: LAST / Resolution: 2.01→33.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 80 307 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192278
X-RAY DIFFRACTIONr_bond_other_d0.0010.022186
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9593097
X-RAY DIFFRACTIONr_angle_other_deg0.77135052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9775256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.15125.701107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1315397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.891157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02519
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_it2.1633.6911021
X-RAY DIFFRACTIONr_mcbond_other2.1643.6831020
X-RAY DIFFRACTIONr_mcangle_it3.5178.2571275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2573.9481257
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: 2.01→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 73 -
Rwork0.316 1228 -
obs--96.94 %

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