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- PDB-5d26: First bromodomain of BRD4 bound to inhibitor XD28 -

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Basic information

Entry
Database: PDB / ID: 5d26
TitleFirst bromodomain of BRD4 bound to inhibitor XD28
ComponentsBromodomain-containing protein 4
KeywordsTRANSCRIPTION / Gene regulation / Bromodomain / Inhibitor
Function / homology
Function and homology information


histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / negative regulation of DNA damage checkpoint / P-TEFb complex binding / histone H3K9ac reader activity / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / 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 / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / p53 binding / Regulation of PD-L1(CD274) transcription / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / DNA damage response / positive regulation of DNA-templated transcription / chromatin / enzyme binding / positive regulation of transcription by RNA polymerase II / DNA-templated transcription / 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
(R,R)-2,3-BUTANEDIOL / Chem-L28 / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.82 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 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)15,6975
Polymers15,0991
Non-polymers5984
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-2 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.470, 49.590, 58.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 15099.380 Da / Num. of mol.: 1 / Mutation: T43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O60885

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Non-polymers , 5 types, 171 molecules

#2: Chemical ChemComp-L28 / N~2~-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-5-methyl-1H-pyrrole-2,4-dicarboxamide


Mass: 422.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O5S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.89 Å3/Da / Density % sol: 34.76 %
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: Oct 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.82→12.4 Å / Num. obs: 10724 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.5
Reflection shellResolution: 1.82→1.92 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1515 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
SCALA3.3.21data scaling
PHASER2.5.6phasing
iMOSFLMdata reduction
RefinementResolution: 1.82→12.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.777 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18747 1033 9.7 %RANDOM
Rwork0.15881 ---
obs0.16168 9658 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.558 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0 Å20 Å2
2--0.43 Å20 Å2
3----0.6 Å2
Refinement stepCycle: 1 / Resolution: 1.82→12.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 40 167 1269
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.021161
X-RAY DIFFRACTIONr_bond_other_d0.0010.021112
X-RAY DIFFRACTIONr_angle_refined_deg1.2192.011587
X-RAY DIFFRACTIONr_angle_other_deg0.74332570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8515134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7272655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05315204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.643153
X-RAY DIFFRACTIONr_chiral_restr0.060.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211309
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
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_it0.1810.677524
X-RAY DIFFRACTIONr_mcbond_other0.180.675523
X-RAY DIFFRACTIONr_mcangle_it0.3211.013659
X-RAY DIFFRACTIONr_mcangle_other0.3211.014660
X-RAY DIFFRACTIONr_scbond_it0.2270.739637
X-RAY DIFFRACTIONr_scbond_other0.2270.74638
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.3711.089928
X-RAY DIFFRACTIONr_long_range_B_refined2.8257.0515030
X-RAY DIFFRACTIONr_long_range_B_other2.5016.6384867
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.817→1.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 64 -
Rwork0.215 682 -
obs--97.26 %
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)
19.36930.622-8.89363.12320.552212.25040.130.19320.11060.0775-0.00650.2286-0.1593-0.5203-0.12350.04440.0169-0.02450.06550.00560.0472-1.319961.23778.5652
23.08080.13890.14710.36630.71014.6473-0.04120.22860.1396-0.10730.01250.0158-0.15540.2220.02870.0348-0.0030.00520.03240.00120.043618.481552.61490.1926
31.295-0.1108-1.05370.85110.44582.1159-0.03960.0403-0.09370.0445-0.01640.06210.0466-0.10650.0560.0114-0.00580.00140.00770.00110.01418.600657.029113.1741
41.0018-0.5307-0.19191.96341.00494.01380.0507-0.02630.05830.05690.0587-0.1361-0.19050.0893-0.10940.024-0.0053-0.0040.0049-0.00130.017813.754163.673118.6538
55.554-0.6778-4.62013.4928-1.33688.6509-0.176-0.0831-0.0859-0.0710.0975-0.20930.09210.4630.07860.0487-0.0237-0.03960.0733-0.01690.104625.99756.447413.119
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 49
2X-RAY DIFFRACTION2A50 - 70
3X-RAY DIFFRACTION3A71 - 122
4X-RAY DIFFRACTION4A123 - 152
5X-RAY DIFFRACTION5A153 - 168

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