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- PDB-4uye: BROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-dimethyl-2-oxo-6-(piperidin... -

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Basic information

Entry
Database: PDB / ID: 4uye
TitleBROMODOMAIN OF HUMAN BRPF1 WITH N-1,3-dimethyl-2-oxo-6-(piperidin-1- yl)-2,3-dihydro-1H-1,3-benzodiazol-5-yl-2-methoxybenzamide
ComponentsPEREGRIN
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / ANTAGONIST
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Regulation of TP53 Activity through Acetylation / HATs acetylate histones / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. ...BRPF1, PHD domain / Peregrin, ePHD domain / : / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChung, C. / Bamborough, P. / Demont, E.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: 1,3-Dimethyl Benzimidazolones are Potent, Selective Inhibitors of the Brpf1 Bromodomain.
Authors: Demont, E.H. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Fallon, D. / Gordon, L.J. / Grandi, P. / Hobbs, C.I. / Hussain, J. / Jones, E.J. / Le Gall, A. / Michon, A.M. / Mitchell, D.J. / ...Authors: Demont, E.H. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Fallon, D. / Gordon, L.J. / Grandi, P. / Hobbs, C.I. / Hussain, J. / Jones, E.J. / Le Gall, A. / Michon, A.M. / Mitchell, D.J. / Prinjha, R.K. / Roberts, A.D. / Sheppard, R.J. / Watson, R.J.
History
DepositionAug 30, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PEREGRIN
B: PEREGRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7035
Polymers27,8522
Non-polymers8513
Water4,324240
1
A: PEREGRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3823
Polymers13,9261
Non-polymers4572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PEREGRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3202
Polymers13,9261
Non-polymers3941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.060, 68.120, 58.750
Angle α, β, γ (deg.)90.00, 126.10, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PEREGRIN / BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1 / PROTEIN BR140


Mass: 13925.918 Da / Num. of mol.: 2 / Fragment: BROMODOMAIN, UNP RESIDUES 622-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-9F9 / N-[1,3-dimethyl-2-oxo-6-(piperidin-1-yl)-2,3-dihydro-1H-benzimidazol-5-yl]-2-methoxybenzamide


Mass: 394.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.58 Å3/Da / Density % sol: 54.42 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES/IMIDAZOLE PH 6.5, 10% MORPHEUS DIVALENTS MPD_P1K_P3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→49.47 Å / Num. obs: 32628 / % possible obs: 75.7 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→49.47 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.037 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20113 1639 5 %RANDOM
Rwork0.17569 ---
obs0.17693 30953 95.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.793 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 62 240 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191962
X-RAY DIFFRACTIONr_bond_other_d0.0010.021370
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9482656
X-RAY DIFFRACTIONr_angle_other_deg0.8233319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8135225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3724.34106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32315347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5191516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 120 -
Rwork0.227 2181 -
obs--93.46 %
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)
10.5890.06780.37951.55530.22130.2855-0.0459-0.0101-0.0831-0.08220.09410.0736-0.06410.031-0.04810.1054-0.0256-0.00360.04230.00580.26961.494258.461816.6999
20.14070.13980.16221.6308-0.12280.3173-0.0415-0.0108-0.04450.02940.0444-0.0957-0.0533-0.0717-0.00290.13140.0025-0.00450.036-0.00410.2442-19.036459.79566.7571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A629 - 737
2X-RAY DIFFRACTION2B629 - 737

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