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- PDB-5dw1: X-ray crystal structure of human BRD2(BD2) in complex with RVX297... -

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Basic information

Entry
Database: PDB / ID: 5dw1
TitleX-ray crystal structure of human BRD2(BD2) in complex with RVX297 to 1.55 A resolution
ComponentsBromodomain-containing protein 2BRD2
KeywordsPROTEIN BINDING/INHIBITOR / bromodomain / PROTEIN BINDING-INHIBITOR complex
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-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-5GD / Bromodomain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWhite, A. / Fontano, E. / Suto, R.K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: RVX-297- a novel BD2 selective inhibitor of BET bromodomains.
Authors: Kharenko, O.A. / Gesner, E.M. / Patel, R.G. / Norek, K. / White, A. / Fontano, E. / Suto, R.K. / Young, P.R. / McLure, K.G. / Hansen, H.C.
History
DepositionSep 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)55,01310
Polymers53,2734
Non-polymers1,7406
Water10,503583
1
A: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7422
Polymers13,3181
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7422
Polymers13,3181
Non-polymers4241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7653
Polymers13,3181
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bromodomain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7653
Polymers13,3181
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.289, 57.318, 62.033
Angle α, β, γ (deg.)62.090, 72.080, 66.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bromodomain-containing protein 2 / BRD2 / O27.1.1 / Really interesting new gene 3 protein


Mass: 13318.358 Da / Num. of mol.: 4 / Fragment: BD2 (UNP residues 345-455)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD2, KIAA9001, RING3 / Plasmid: PJEXPRESS401 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P25440
#2: Chemical
ChemComp-5GD / 2-{3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}-5,7-dimethoxyquinazolin-4(3H)-one


Mass: 423.505 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H29N3O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 3 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.6 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2011 / Details: Mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 85026 / % possible obs: 95 % / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Χ2: 1.033 / Net I/av σ(I): 17.029 / Net I/σ(I): 14.2 / Num. measured all: 165868
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.6120.42683330.6450.4260.6021.02493.6
1.61-1.6720.29684500.8020.2960.4181.05594
1.67-1.7520.22184350.8790.2210.3121.06694.7
1.75-1.8420.14585240.9440.1450.2051.06795.1
1.84-1.9520.09685580.9720.0960.1361.04495.6
1.95-2.120.06385640.9870.0630.091.06595.8
2.1-2.321.90.04886790.990.0480.0681.02396.7
2.32-2.651.90.04186700.9920.0410.0581.00697
2.65-3.341.90.03487130.9940.0340.0480.98497.4
3.34-501.90.02981000.9940.0290.0410.99590.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2116 / WRfactor Rwork: 0.1718 / FOM work R set: 0.8641 / SU B: 1.386 / SU ML: 0.049 / SU R Cruickshank DPI: 0.0682 / SU Rfree: 0.0738 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1948 4250 5 %RANDOM
Rwork0.1589 ---
obs0.1607 80774 94.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.82 Å2 / Biso mean: 28.174 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20.23 Å20.13 Å2
2--0.28 Å2-0.34 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 126 583 4350
Biso mean--27.37 40.55 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194036
X-RAY DIFFRACTIONr_bond_other_d0.0030.023814
X-RAY DIFFRACTIONr_angle_refined_deg2.2131.9875473
X-RAY DIFFRACTIONr_angle_other_deg1.11238812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0635475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40623.467199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98215710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9811525
X-RAY DIFFRACTIONr_chiral_restr0.1310.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0214504
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02965
X-RAY DIFFRACTIONr_mcbond_it2.2262.4051829
X-RAY DIFFRACTIONr_mcbond_other2.2252.4051830
X-RAY DIFFRACTIONr_mcangle_it3.063.5862295
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 302 -
Rwork0.254 5678 -
all-5980 -
obs--90.1 %

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