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- PDB-5d3j: First bromodomain of BRD4 bound to inhibitor XD33 -

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Basic information

Entry
Database: PDB / ID: 5d3j
TitleFirst bromodomain of BRD4 bound to inhibitor XD33
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Gene regulation / Bromodomain / Inhibitor
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-L33 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsWohlwend, D. / Huegle, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationWO2012/1-1 Germany
CitationJournal: J.Med.Chem. / Year: 2016
Title: 4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1).
Authors: Hugle, M. / Lucas, X. / Weitzel, G. / Ostrovskyi, D. / Breit, B. / Gerhardt, S. / Einsle, O. / Gunther, S. / Wohlwend, D.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,4182
Polymers15,0121
Non-polymers4061
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.290, 49.520, 58.150
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


Mass: 15012.301 Da / Num. of mol.: 1 / Fragment: UNP residues 43-168 / Mutation: T43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Chemical ChemComp-L33 / 4-acetyl-N-[3-(diethylsulfamoyl)phenyl]-3-ethyl-5-methyl-1H-pyrrole-2-carboxamide


Mass: 405.511 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Hepes, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→32.6 Å / Num. obs: 14195 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.3
Reflection shellResolution: 1.65→1.74 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2017 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALA3.3.21data scaling
PHASER2.5.6phasing
iMOSFLMdata reduction
RefinementResolution: 1.7→32.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.509 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20554 1296 10 %RANDOM
Rwork0.17712 ---
obs0.17989 11689 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.711 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.7→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1055 0 28 148 1231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021147
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9981571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3775133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15726.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.089153
X-RAY DIFFRACTIONr_chiral_restr0.0830.2163
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022903
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3930.899523
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6591.342659
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7481.033624
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.3969.3624997
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 82 -
Rwork0.274 851 -
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)
112.5708-1.6854-8.18367.30620.48439.12870.02610.4228-0.05730.0749-0.06380.15530.1849-0.52470.03770.0385-0.0133-0.02910.06380.0060.0437-0.399360.52667.6339
24.4113-0.4581-3.98170.05970.527311.20710.05330.42020.73220.0011-0.0947-0.05-0.7724-0.56710.04130.1162-0.0462-0.02230.2027-0.00740.21419.541856.9483-6.1771
30.65290.12851.51562.3747-2.21758.4189-0.01650.1363-0.1465-0.12160.0237-0.08810.20940.2847-0.00720.0426-0.00130.01860.033-0.03340.068522.421650.33332.3599
47.5937-1.254-0.12372.13310.13752.55320.0243-0.1726-0.33440.14530.0048-0.01440.28740.0215-0.02910.05440.0019-0.0030.00470.00940.021413.09651.373818.494
56.69623.2275-4.27584.7473-2.30696.08850.01460.05560.0180.19220.04670.317-0.2137-0.2861-0.06130.03480.02210.00780.06980.00130.0404-0.499164.938317.3845
62.725-1.0963-2.66560.5661.60875.0370.02240.09490.0042-0.03550.00270.0006-0.08550.0043-0.02520.0285-0.0328-0.0150.04270.01740.009614.446757.6296.0896
71.46180.08761.84012.8834-0.65885.23730.0006-0.16660.01890.2063-0.024-0.0093-0.0426-0.0280.02340.0209-0.0046-0.00380.056-0.00120.001910.9165.161424.186
811.512-2.8212-7.89163.85481.45359.70590.0191-0.17380.16310.04210.1168-0.3046-0.03460.3428-0.13590.0412-0.0069-0.03760.0566-0.00120.05523.52457.43818.3874
94.2414-0.47121.04155.09781.34698.982-0.22620.2108-0.0785-0.3625-0.1746-0.06720.45830.33070.40080.1457-00.01060.16450.00410.186130.580654.88743.7331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 49
2X-RAY DIFFRACTION2A50 - 56
3X-RAY DIFFRACTION3A57 - 69
4X-RAY DIFFRACTION4A70 - 86
5X-RAY DIFFRACTION5A87 - 103
6X-RAY DIFFRACTION6A104 - 133
7X-RAY DIFFRACTION7A134 - 150
8X-RAY DIFFRACTION8A151 - 162
9X-RAY DIFFRACTION9A163 - 168

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