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- PDB-8wyg: Crystal Structure of the second bromodomain of human BRD2 in comp... -

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Basic information

Entry
Database: PDB / ID: 8wyg
TitleCrystal Structure of the second bromodomain of human BRD2 in complex with the inhibitor 22
ComponentsBromodomain-containing protein 2BRD2
KeywordsPROTEIN BINDING / BRD2(2) / Bromodomain
Function / homology
Function and homology information


chromatin looping / acetylation-dependent protein binding / 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 ...chromatin looping / acetylation-dependent protein binding / 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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. ...NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Chem-XHN / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsXu, H. / Zhao, X. / Shen, H. / Xu, Y. / Wu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22307116 China
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Novel Phenoxyaryl Pyridones as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with High Selectivity for the Second Bromodomain (BD2) to Potentially Treat Acute Myeloid Leukemia.
Authors: Jiang, W. / Hou, Q. / Xu, H. / Yang, K. / Wang, X. / Zhang, K. / Zeng, Y. / Li, W. / Wang, B. / Luo, G. / Zhao, X. / Shen, H. / Xu, Y. / Wu, X.
History
DepositionOct 30, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_initial_refinement_model / refine
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_initial_refinement_model.entity_id_list / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 2
B: Bromodomain-containing protein 2
C: Bromodomain-containing protein 2
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1318
Polymers63,9254
Non-polymers2,2074
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.782, 95.497, 109.080
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 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 15981.218 Da / Num. of mol.: 4
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-XHN / 2-[[5-[2-(4-fluoranyl-2,6-dimethyl-phenoxy)-5-(2-oxidanylpropan-2-yl)phenyl]-1-methyl-2-oxidanylidene-pyridin-4-yl]amino]-~{N}-(4-oxidanylcyclohexyl)ethanamide


Mass: 551.649 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H38FN3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.74 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 60% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.13→109.08 Å / Num. obs: 17520 / % possible obs: 100 % / Redundancy: 6 % / CC1/2: 0.951 / Rmerge(I) obs: 0.364 / Rpim(I) all: 0.163 / Rrim(I) all: 0.4 / Net I/σ(I): 5.9 / Num. measured all: 104944
Reflection shellResolution: 3.13→3.35 Å / % possible obs: 100 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.726 / Num. measured all: 19315 / Num. unique obs: 3115 / CC1/2: 0.717 / Rpim(I) all: 0.317 / Rrim(I) all: 0.794 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7wni

7wni


Resolution: 3.13→71.85 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.872 / SU B: 19.374 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.03 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25677 931 5.3 %RANDOM
Rwork0.19452 ---
obs0.19786 16542 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.416 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å20 Å2
2---1.4 Å20 Å2
3----2.51 Å2
Refinement stepCycle: 1 / Resolution: 3.13→71.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 160 1 3792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193903
X-RAY DIFFRACTIONr_bond_other_d0.0040.023595
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9985273
X-RAY DIFFRACTIONr_angle_other_deg1.1233.0138337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0245435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73423.404188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.17215676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5491524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214221
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02827
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_it3.1634.9411764
X-RAY DIFFRACTIONr_mcbond_other3.1624.9411765
X-RAY DIFFRACTIONr_mcangle_it5.1217.42191
X-RAY DIFFRACTIONr_mcangle_other5.127.42192
X-RAY DIFFRACTIONr_scbond_it3.7075.3022139
X-RAY DIFFRACTIONr_scbond_other3.7065.3012140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1427.7453083
X-RAY DIFFRACTIONr_long_range_B_refined8.69455.6654597
X-RAY DIFFRACTIONr_long_range_B_other8.69355.6664598
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.13→3.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 73 -
Rwork0.294 1204 -
obs--100 %

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