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- PDB-4lzs: Crystal Structure of BRD4(1) bound to inhibitor XD46 -

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Basic information

Entry
Database: PDB / ID: 4lzs
TitleCrystal Structure of BRD4(1) bound to inhibitor XD46
ComponentsBromodomain-containing protein 4BRD4
KeywordsPROTEIN BINDING/INHIBITOR / BRD4 inhibitor / bromodomain / epigenetic reader protein / acetylated lysine / histone tail / nucleus / PROTEIN BINDING-INHIBITOR complex
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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity ...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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / 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 / 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 protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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-L46 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsWohlwend, D. / Huegle, M. / Einsle, O. / Gerhardt, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: 4-Acyl pyrroles: mimicking acetylated lysines in histone code reading.
Authors: Lucas, X. / Wohlwend, D. / Hugle, M. / Schmidtkunz, K. / Gerhardt, S. / Schule, R. / Jung, M. / Einsle, O. / Gunther, S.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3082
Polymers15,0991
Non-polymers2081
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.420, 43.900, 77.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: FIRST BROMODOMAIN DOMAIN (UNP RESIDUES 44-168)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60885
#2: Chemical ChemComp-L46 / 4-acetyl-3-ethyl-N,5-dimethyl-1H-pyrrole-2-carboxamide


Mass: 208.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: NaCitrate, PEG 3,350, pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 11, 2013 / Details: VARIMAX VHF Focussing mirrors
RadiationMonochromator: VariMax VHF focusing mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.2→38.765 Å / Num. obs: 6808 / % possible obs: 99.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.2-2.282.90.3073.3186164699.7
8.52-12.42.60.06310.12459467.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.27 Å12.4 Å
Translation5.27 Å12.4 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→12.4 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2346 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8346 / SU B: 12.81 / SU ML: 0.177 / SU R Cruickshank DPI: 0.357 / SU Rfree: 0.2326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 320 4.7 %RANDOM
Rwork0.1921 ---
obs0.1946 6785 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.61 Å2 / Biso mean: 13.5877 Å2 / Biso min: 5.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å2-0 Å2
2---0.65 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→12.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 15 92 1169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021124
X-RAY DIFFRACTIONr_bond_other_d0.0010.021072
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9861533
X-RAY DIFFRACTIONr_angle_other_deg0.77132480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.38225.92654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64615201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.166153
X-RAY DIFFRACTIONr_chiral_restr0.0690.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211270
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02250
X-RAY DIFFRACTIONr_mcbond_it0.1620.703517
X-RAY DIFFRACTIONr_mcbond_other0.1610.701516
X-RAY DIFFRACTIONr_mcangle_it0.2921.051648
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 27 -
Rwork0.202 431 -
all-458 -
obs--99.35 %
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)
10.57780.32520.25520.3173-0.30881.68490.0262-0.01660.08270.0664-0.03810.0509-0.06730.00760.01180.0807-0.0125-0.00540.05750.02280.067413.597944.201997.8405
20.9543-0.4879-0.20312.40660.53391.113-0.07750.003-0.0310.0501-0.00340.10030.0018-0.09180.08090.0082-0.0025-0.00020.0172-0.00040.010510.125443.908983.6691
31.25570.3971.17612.82212.61963.6206-0.0353-0.13110.0050.0677-0.01290.0775-0.0152-0.20480.04820.0490.0013-0.02290.0490.01840.023712.357750.431492.7893
41.09990.03040.43692.96330.66811.0655-0.07950.15910.052-0.2850.02250.1067-0.1730.08560.05690.0552-0.0140.00090.06510.02180.028214.119949.453775.963
52.78253.087-3.6214.22380.235727.66240.126-0.16640.07960.0256-0.30990.152-0.7687-0.68240.18390.10620.02620.00620.1494-0.0010.154910.948565.899992.1407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 61
2X-RAY DIFFRACTION2A62 - 109
3X-RAY DIFFRACTION3A110 - 132
4X-RAY DIFFRACTION4A133 - 162
5X-RAY DIFFRACTION5A163 - 168

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