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- PDB-6dml: A multiconformer ligand model of 3,5 dimethylisoxaxole bound to t... -

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Basic information

Entry
Database: PDB / ID: 6dml
TitleA multiconformer ligand model of 3,5 dimethylisoxaxole bound to the bromodomain of human BRD4
ComponentsBromodomain-containing protein 4
Keywordstranscription/transcription inhibitor / Complex / multiconformer model / TRANSCRIPTION / transcription-transcription 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / RNA polymerase II CTD heptapeptide repeat kinase activity / histone reader 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 / 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 / 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-9BM / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsHudson, B.M. / van Zundert, G. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
Citation
Journal: J. Med. Chem. / Year: 2018
Title: qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Authors: van Zundert, G.C.P. / Hudson, B.M. / de Oliveira, S.H.P. / Keedy, D.A. / Fonseca, R. / Heliou, A. / Suresh, P. / Borrelli, K. / Day, T. / Fraser, J.S. / van den Bedem, H.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 1, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.name
Remark 0THIS ENTRY 6DML REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4BW3, DETERMINED BY C. ...THIS ENTRY 6DML REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 4BW3, DETERMINED BY C.CHUNG,O.MIRGUET,Y.LAMOTTE,P.BAMBOROUGH,D.DELANNEE,A.BOUILLOT,F.GELLIBERT,G.KRYSA,A.LEWIS,J.WITHERINGTON,P.HUET,Y.DUDIT,L.TROTTET,E.NICODEME

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7325
Polymers15,0991
Non-polymers6334
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.570, 48.850, 61.020
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: 15099.380 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9BM / 4-((2-(tert-butyl)phenyl)amino)-7-(3,5-dimethylisoxazol-4-yl)-6-methoxy-1,5-naphthyridine-3-carboxylic acid


Mass: 446.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H26N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.15 Å3/Da / Density % sol: 42.8 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 5CFW
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG3350, 0.2M NANO3, 0.1M BIS-TRIS-PROPANE PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→38.14 Å / Num. obs: 21405 / % possible obs: 15.5 % / Redundancy: 6.4 % / Net I/σ(I): 15.5
Reflection shellResolution: 1.5→1.58 Å

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Processing

Software
NameVersionClassification
PHENIX1.11_2558refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.5→38.135 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.94
RfactorNum. reflection% reflection
Rfree0.1923 1098 5.13 %
Rwork0.1453 --
obs0.1476 21405 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 82.57 Å2 / Biso mean: 32.1895 Å2 / Biso min: 12.43 Å2
Refinement stepCycle: final / Resolution: 1.5→38.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 146 190 1397
Biso mean--49.08 45.53 -
Num. residues----127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111190
X-RAY DIFFRACTIONf_angle_d1.3061627
X-RAY DIFFRACTIONf_chiral_restr0.056162
X-RAY DIFFRACTIONf_plane_restr0.007204
X-RAY DIFFRACTIONf_dihedral_angle_d12.5707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.56830.23661460.168824862632100
1.5683-1.6510.19741370.152924582595100
1.651-1.75440.20241430.144925212664100
1.7544-1.88990.20071140.138725272641100
1.8899-2.080.17241530.136525122665100
2.08-2.3810.19611330.130725352668100
2.381-2.99960.19681220.149725932715100
2.9996-38.14740.18771500.14922675282599

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