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- PDB-5d3h: First bromodomain of BRD4 bound to inhibitor XD29 -

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Basic information

Entry
Database: PDB / ID: 5d3h
TitleFirst bromodomain of BRD4 bound to inhibitor XD29
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 / 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 / condensed nuclear chromosome / histone reader activity / : ...RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / 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 / condensed nuclear chromosome / histone reader activity / : / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / p53 binding / 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 / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-57G / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWohlwend, D. / Huegle, M. / Weitzel, G.
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 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)15,4502
Polymers15,0121
Non-polymers4381
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.350, 49.090, 57.960
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: First bromodomain, UNP residues 44-168
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-57G / N-[5-(diethylsulfamoyl)-2-hydroxyphenyl]-3-ethyl-4-(hydroxyacetyl)-5-methyl-1H-pyrrole-2-carboxamide


Mass: 437.510 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 1.86 Å3/Da / Density % sol: 34.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Bis-tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→27.1 Å / Num. obs: 11275 / % possible obs: 88.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 10.9
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 2.4 / Num. unique all: 475 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimless0.2.17data scaling
PHASER2.5.6phasing
iMOSFLM7.0.9data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model of apo-BRD4(1)

Resolution: 1.7→27.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.612 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19644 1115 9.9 %RANDOM
Rwork0.16188 ---
obs0.16531 10137 87.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.7→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1046 0 30 146 1222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021151
X-RAY DIFFRACTIONr_bond_other_d0.0020.021089
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9981577
X-RAY DIFFRACTIONr_angle_other_deg0.76732520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4565134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91126.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37615202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.117153
X-RAY DIFFRACTIONr_chiral_restr0.0660.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211320
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02261
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_it0.4210.58524
X-RAY DIFFRACTIONr_mcbond_other0.4170.579523
X-RAY DIFFRACTIONr_mcangle_it0.5230.87662
X-RAY DIFFRACTIONr_mcangle_other0.5230.87663
X-RAY DIFFRACTIONr_scbond_it0.5580.67627
X-RAY DIFFRACTIONr_scbond_other0.5560.666625
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.6860.993916
X-RAY DIFFRACTIONr_long_range_B_refined1.2976.2825019
X-RAY DIFFRACTIONr_long_range_B_other0.9795.9114890
X-RAY DIFFRACTIONr_rigid_bond_restr1.37732240
X-RAY DIFFRACTIONr_sphericity_free13.536518
X-RAY DIFFRACTIONr_sphericity_bonded3.12852332
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 71 -
Rwork0.215 610 -
obs--73.7 %
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)
15.424-2.0584-0.94617.78615.05316.69850.0280.74220.091-0.04590.05590.25090.0592-0.8261-0.08390.0433-0.0154-0.02480.36920.09410.04540.620959.09226.7226
24.76991.79523.15740.84271.91515.2562-0.14740.10620.2522-0.0376-0.02140.0994-0.0152-0.21430.16870.1118-0.05060.00870.0650.03750.099216.338654.1199-5.8058
34.30131.1928-1.83080.3369-0.58526.1843-0.0849-0.0679-0.0943-0.0391-0.0272-0.04250.21980.17940.11210.06860.0150.01420.01440.02960.081420.671849.70119.2058
46.7689-3.32340.77042.6427-0.43522.0495-0.1327-0.2088-0.06020.22770.00650.01060.13-0.05580.12620.0756-0.01260.01210.03320.01950.02969.304152.895819.8013
56.62943.317-1.38766.57-1.18851.75250.11720.0207-0.0030.3134-0.0885-0.06410.1404-0.2025-0.02870.13590.03370.05010.1944-0.00690.0628-3.738361.098920.974
62.3693-0.0918-1.57870.95291.51893.29590.0847-0.02690.07590.0071-0.10440.0465-0.031-0.15680.01970.0333-0.0129-0.01490.02640.00570.01917.342460.528710.9444
72.0502-1.3023-2.5032.27422.73745.59960.0386-0.04540.0605-0.0210.0563-0.0677-0.1579-0.0077-0.09490.0313-0.007-0.01680.01240.00750.016214.991460.70028.9956
83.2666-2.1401-4.04924.61236.08968.70180.2082-0.04830.08430.0257-0.0594-0.0941-0.064-0.0466-0.14870.13870.0063-0.03250.07560.01360.046813.097861.709626.3315
96.4268-0.6351-1.7252.50461.36923.26360.0383-0.12530.0840.0564-0.018-0.22670.04050.0714-0.02030.07870-0.02190.08050.00180.081624.281256.514817.4436
103.5746-0.18060.25881.82611.682312.4034-0.2292-0.0495-0.0974-0.1399-0.1831-0.1720.46410.40230.41230.10470.00590.01540.1490.03180.171130.414654.88266.7891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 51
2X-RAY DIFFRACTION2A52 - 61
3X-RAY DIFFRACTION3A62 - 75
4X-RAY DIFFRACTION4A76 - 89
5X-RAY DIFFRACTION5A90 - 96
6X-RAY DIFFRACTION6A97 - 114
7X-RAY DIFFRACTION7A115 - 140
8X-RAY DIFFRACTION8A141 - 153
9X-RAY DIFFRACTION9A154 - 161
10X-RAY DIFFRACTION10A162 - 167

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