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- PDB-8z69: Crystal Structure of the second bromodomain of human BRD2 BD2 in ... -

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Basic information

Entry
Database: PDB / ID: 8z69
TitleCrystal Structure of the second bromodomain of human BRD2 BD2 in complex with the inhibitor Y13195
ComponentsBRD2_HUMAN
KeywordsPROTEIN BINDING / BRD2 / BD2 / Bromodomain
Function / homology
Function and homology information


histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly ...histone H4K12ac reader activity / histone H4K5ac reader activity / histone H3K14ac reader activity / 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 / nucleosome assembly / spermatogenesis / histone binding / nuclear speck / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain ...Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
: / FORMIC ACID / DI(HYDROXYETHYL)ETHER / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLi, J. / Hu, Q. / Xu, H. / Zhao, X. / Zhang, C. / Zhu, R. / Wu, X. / Zhang, Y. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81673357 China
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of the First BRD4 Second Bromodomain (BD2)-Selective Inhibitors.
Authors: Li, J. / Hu, Q. / Zhu, R. / Dong, R. / Shen, H. / Hu, J. / Zhang, C. / Zhang, X. / Xu, T. / Xiang, Q. / Zhang, Y. / Lin, B. / Zhao, L. / Wu, X. / Xu, Y.
History
DepositionApr 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRD2_HUMAN
B: BRD2_HUMAN
C: BRD2_HUMAN
D: BRD2_HUMAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,59532
Polymers63,9254
Non-polymers3,67028
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.270, 95.530, 110.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
BRD2_HUMAN / 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
Details: BRD2_HUMAN, P25440,BD2 sequence from 320-343 are tags. EGDIHMKKGHHHHHHENLYFQGGS
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Production host: Escherichia coli (E. coli) / References: UniProt: P25440

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Non-polymers , 7 types, 422 molecules

#2: Chemical
ChemComp-A1L0Y / 7-(2-(4-fluoro-2,6-dimethylphenoxy)-5-(2-hydroxypropan-2-yl)phenyl)-5-methyl-2-(2-phenyl-1H-imidazol-5-yl)furo[3,2-c]pyridin-4(5H)-one


Mass: 563.618 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H30FN3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5 M Sodium formate, 0.1 M Sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.77→42.24 Å / Num. obs: 91270 / % possible obs: 98.5 % / Redundancy: 11.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.052 / Χ2: 0.9 / Net I/σ(I): 23.6
Reflection shellResolution: 1.77→1.8 Å / % possible obs: 84.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 1.04 / Num. measured all: 20828 / Num. unique obs: 3819 / CC1/2: 0.616 / Rpim(I) all: 0.47 / Rrim(I) all: 1.147 / Χ2: 0.74 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WNI

7wni


Resolution: 1.77→42.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.863 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19904 4442 4.9 %RANDOM
Rwork0.18108 ---
obs0.18196 86753 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.721 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å20 Å20 Å2
2---0.57 Å20 Å2
3----1.3 Å2
Refinement stepCycle: 1 / Resolution: 1.77→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 259 394 4267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134060
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183699
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.7225472
X-RAY DIFFRACTIONr_angle_other_deg1.3451.648571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0485457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.36421.826219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77615691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5331525
X-RAY DIFFRACTIONr_chiral_restr0.0750.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024428
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02903
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_it2.113.2821774
X-RAY DIFFRACTIONr_mcbond_other2.1093.2851775
X-RAY DIFFRACTIONr_mcangle_it3.0044.8892216
X-RAY DIFFRACTIONr_mcangle_other3.0044.892217
X-RAY DIFFRACTIONr_scbond_it3.3313.7972286
X-RAY DIFFRACTIONr_scbond_other3.333.7892281
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1295.4573246
X-RAY DIFFRACTIONr_long_range_B_refined6.64738.325050
X-RAY DIFFRACTIONr_long_range_B_other6.58637.7294944
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35640.1
12B35640.1
21A36400.08
22C36400.08
31A36050.1
32D36050.1
41B35830.09
42C35830.09
51B35650.1
52D35650.1
61C35720.09
62D35720.09
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 278 -
Rwork0.296 5515 -
obs--85.27 %

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