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- PDB-5u6v: X-ray crystal structure of 1,2,3-triazolobenzodiazepine in comple... -

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Basic information

Entry
Database: PDB / ID: 5u6v
TitleX-ray crystal structure of 1,2,3-triazolobenzodiazepine in complex with BRD2(D2)
ComponentsBromodomain-containing protein 2
Keywordstranscription/transcription inhibitor / Bromodomain / benzodiazepine / epigenetics / transcription-transcription inhibitor complex
Function / homology
Function and homology information


acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck ...acetylation-dependent protein binding / chromatin looping / RUNX3 regulates p14-ARF / positive regulation of T-helper 17 cell lineage commitment / protein localization to chromatin / neural tube closure / lysine-acetylated histone binding / nucleosome assembly / spermatogenesis / nuclear speck / protein phosphorylation / protein serine/threonine kinase activity / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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. ...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-7WY / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.775 Å
AuthorsHatfaludi, T. / Sharp, P.P. / Garnier, J.-M. / Burns, C.J. / Czabotar, P.E.
CitationJournal: ACS Med Chem Lett / Year: 2017
Title: Design, Synthesis, and Biological Activity of 1,2,3-Triazolobenzodiazepine BET Bromodomain Inhibitors.
Authors: Sharp, P.P. / Garnier, J.M. / Hatfaludi, T. / Xu, Z. / Segal, D. / Jarman, K.E. / Jousset, H. / Garnham, A. / Feutrill, J.T. / Cuzzupe, A. / Hall, P. / Taylor, S. / Walkley, C.R. / Tyler, D. ...Authors: Sharp, P.P. / Garnier, J.M. / Hatfaludi, T. / Xu, Z. / Segal, D. / Jarman, K.E. / Jousset, H. / Garnham, A. / Feutrill, J.T. / Cuzzupe, A. / Hall, P. / Taylor, S. / Walkley, C.R. / Tyler, D. / Dawson, M.A. / Czabotar, P. / Wilks, A.F. / Glaser, S. / Huang, D.C.S. / Burns, C.J.
History
DepositionDec 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 6, 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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6287
Polymers12,9151
Non-polymers7136
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.617, 71.743, 31.935
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

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Components

#1: Protein Bromodomain-containing protein 2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 12914.799 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440
#2: Chemical ChemComp-7WY / 5-[7-(4-chlorophenyl)-1-methyl-6,7-dihydro-5H-[1,2,3]triazolo[1,5-d][1,4]benzodiazepin-9-yl]pyridin-2-amine


Mass: 402.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19ClN6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20w/v PEG 4000, 0.1M sodium HEPES pH7.5, 10 v/v2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.77→42.43 Å / Num. obs: 12213 / % possible obs: 99.7 % / Redundancy: 7.1 % / Net I/σ(I): 12.23

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.775→42.429 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1926 1224 10.02 %
Rwork0.1551 --
obs0.1589 12210 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.775→42.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 49 128 1079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006975
X-RAY DIFFRACTIONf_angle_d0.7721307
X-RAY DIFFRACTIONf_dihedral_angle_d11.931590
X-RAY DIFFRACTIONf_chiral_restr0.044126
X-RAY DIFFRACTIONf_plane_restr0.006166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7747-1.84580.23441290.20731165X-RAY DIFFRACTION98
1.8458-1.92980.2221340.17381206X-RAY DIFFRACTION100
1.9298-2.03150.21131330.16321194X-RAY DIFFRACTION100
2.0315-2.15880.20891350.13671203X-RAY DIFFRACTION100
2.1588-2.32550.1791330.14181201X-RAY DIFFRACTION100
2.3255-2.55950.19721370.14491222X-RAY DIFFRACTION100
2.5595-2.92970.18231370.15121232X-RAY DIFFRACTION100
2.9297-3.69080.18361370.14191232X-RAY DIFFRACTION100
3.6908-42.44120.18231490.16731331X-RAY DIFFRACTION100
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)
10.83630.66280.26442.23080.38550.52280.0031-0.0004-0.02060.01910.00750.07590.0104-0.0615-0.00570.06420.01030.01120.07670.01010.0765-13.95732.1138-1.6604
26.3703-0.09963.39292.53060.75787.3553-0.0335-0.32930.02110.3134-0.0170.1694-0.0424-0.09510.00830.13010.00050.03130.08310.02520.0804-12.75397.98149.4537
31.33110.0967-0.53584.25891.78722.2303-0.00490.0488-0.0794-0.04570.02250.01260.0053-0.0229-0.04780.05440.01560.00530.06690.02360.0861-7.587-3.4076-1.8406
43.91411.94941.11524.18881.59142.51660.07090.00590.0929-0.03350.0518-0.1312-0.03860.0109-0.16210.07570.01160.02560.08020.01530.0605-3.18995.6334-5.7651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 347 through 395 )
2X-RAY DIFFRACTION2chain 'A' and (resid 396 through 410 )
3X-RAY DIFFRACTION3chain 'A' and (resid 411 through 433 )
4X-RAY DIFFRACTION4chain 'A' and (resid 434 through 455 )

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