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- PDB-4lyw: Crystal Structure of BRD4(1) bound to inhibitor XD14 -

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Basic information

Entry
Database: PDB / ID: 4lyw
TitleCrystal Structure of BRD4(1) bound to inhibitor XD14
ComponentsBromodomain-containing protein 4
KeywordsPROTEIN BINDING/INHIBITOR / BRD4 inhibitor / bromodomain / epigenetic reader protein / acetylated lysine / histone tail / 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 / 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 / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase 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 / chromatin / 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-21Q / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsWohlwend, D. / Gerhardt, S. / Einsle, O.
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
DepositionJul 31, 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)15,5052
Polymers15,0831
Non-polymers4221
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.810, 47.920, 57.800
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 / Protein HUNK1


Mass: 15083.378 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-21Q / 4-acetyl-N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide


Mass: 421.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: NaFormate, 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: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 13, 2012
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: 1.86→57.8 Å / Num. obs: 8320 / % possible obs: 81.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.545 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.44
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.86-1.910.3453.441037449160.2
1.91-1.960.5891.921586597185.4
1.96-2.020.3792.611558579183.3
2.02-2.080.3293.281563587183.7
2.08-2.150.2524.341526560185.8
2.15-2.230.2025.061449531183.2
2.23-2.310.1726.151381512183.1
2.31-2.410.1656.631357498183.8
2.41-2.510.147.861304484184.3
2.51-2.630.09710.291284472184.9
2.63-2.780.07912.711193442184.5
2.78-2.950.05916.321126418185.8
2.95-3.150.05418.641137415185.4
3.15-3.40.03823.61030375183.9
3.4-3.730.03428.27900333182.2
3.73-4.170.02633.54842302180.5
4.17-4.810.02437.97734268180
4.81-5.890.02237.01634229179.5
5.89-8.330.02235.12500178175.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.66 Å
Translation2.5 Å19.66 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.562 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2176 / WRfactor Rwork: 0.1773 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8412 / SU B: 8.855 / SU ML: 0.135 / SU R Cruickshank DPI: 0.2461 / SU Rfree: 0.1853 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 407 4.9 %RANDOM
Rwork0.1966 ---
obs0.1985 7976 94.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.18 Å2 / Biso mean: 32.1409 Å2 / Biso min: 15.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0 Å20 Å2
2--1.78 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 29 98 1188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021141
X-RAY DIFFRACTIONr_angle_refined_deg1.37321559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1035130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50326.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70515200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.483153
X-RAY DIFFRACTIONr_chiral_restr0.0880.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022915
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 27 -
Rwork0.336 547 -
all-574 -
obs--97.45 %
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)
127.3252-8.5069-10.90576.19160.840919.14970.10.6757-0.23710.10420.05230.2839-0.1333-0.8888-0.15230.0538-0.0046-0.00720.05660.01170.1233-0.395310.04647.5183
29.1011-4.538-3.38092.27271.46886.35090.10730.81550.1978-0.0841-0.3918-0.1090.4576-0.56880.28450.1475-0.0704-0.04130.14130.00850.142310.59766.7382-6.0394
35.89411.6713-3.96123.6885-4.247416.5744-0.02470.1485-0.4630.0289-0.241-0.27740.47170.57730.26570.02270.0134-0.01110.05040.01530.110224.0411.57382.4366
412.7126-1.7546-4.02921.3349-0.20641.8854-0.1331-0.3686-0.79830.1828-0.1711-0.01380.05820.31340.30420.24290.0396-0.07060.12140.08580.158914.52211.703618.5312
58.37753.6716-1.87245.9026-3.2976.48090.2118-0.55440.11480.45650.09320.4641-0.4181-0.3943-0.3050.10250.05110.00420.11020.0280.0785-0.191213.963816.844
63.5209-0.7773-2.07521.57440.27224.91690.07590.0226-0.07710.0017-0.0758-0.05570.01310.104-0.00020.0156-0.0048-0.02240.00980.01060.034215.34388.43766.5944
76.1868-0.34752.81631.75971.84574.1112-0.6194-1.06470.43170.63610.25620.129-0.1727-0.10350.36320.9051-0.0240.03420.273-0.05050.067810.742315.1125.0211
817.0046-2.816-11.28894.7910.52677.9119-0.1122-0.90930.10950.44840.1361-0.2323-0.06160.6048-0.02390.1311-0.0394-0.10270.19730.0480.124424.82978.47518.0532
914.650512.08028.849916.6656-3.593723.0385-0.55330.5569-1.1333-0.69790.6839-1.2359-0.0410.0568-0.13060.18220.06130.03280.17740.05660.305931.91956.14021.8348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 49
2X-RAY DIFFRACTION2A50 - 56
3X-RAY DIFFRACTION3A57 - 69
4X-RAY DIFFRACTION4A70 - 86
5X-RAY DIFFRACTION5A87 - 103
6X-RAY DIFFRACTION6A104 - 135
7X-RAY DIFFRACTION7A136 - 150
8X-RAY DIFFRACTION8A151 - 163
9X-RAY DIFFRACTION9A164 - 168

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