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- PDB-5ov8: Crystal structure of the human BRPF1 bromodomain in complex with BZ097 -

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Basic information

Entry
Database: PDB / ID: 5ov8
TitleCrystal structure of the human BRPF1 bromodomain in complex with BZ097
ComponentsPeregrin
KeywordsDNA BINDING PROTEIN / Bromodomain and PHD finger-containing protein 1(BRPF1) / monocytic leukemia zinc-finger (MOZ) / Inhibitor / transcription
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
Chem-AXN / NITRATE ION / Peregrin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhu, J. / Caflisch, A.
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-based discovery of selective BRPF1 bromodomain inhibitors.
Authors: Zhu, J. / Zhou, C. / Caflisch, A.
History
DepositionAug 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peregrin
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4115
Polymers27,4072
Non-polymers1,0033
Water4,954275
1
A: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2363
Polymers13,7041
Non-polymers5332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peregrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1742
Polymers13,7041
Non-polymers4711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.195, 56.538, 48.595
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peregrin / Bromodomain and PHD finger-containing protein 1 / Protein Br140


Mass: 13703.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRPF1, BR140 / Production host: Escherichia coli (E. coli) / References: UniProt: P55201
#2: Chemical ChemComp-AXN / ~{N}-[1,4-dimethyl-2,3-bis(oxidanylidene)-7-pyrrolidin-1-yl-quinoxalin-6-yl]-4-(2-methylpropyl)benzenesulfonamide


Mass: 470.584 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30N4O4S
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris Propane pH9, 10% EG, 0.15M NaNO3, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.8→47.46 Å / Num. obs: 23018 / % possible obs: 97.1 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1295 / CC1/2: 0.946 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LC2

4lc2


Resolution: 1.8→47.459 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 24.4
RfactorNum. reflection% reflection
Rfree0.2439 1991 8.66 %
Rwork0.1966 --
obs0.2007 22987 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 70 275 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061954
X-RAY DIFFRACTIONf_angle_d0.8042645
X-RAY DIFFRACTIONf_dihedral_angle_d10.3231445
X-RAY DIFFRACTIONf_chiral_restr0.046279
X-RAY DIFFRACTIONf_plane_restr0.005340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.31541380.23011415X-RAY DIFFRACTION93
1.845-1.89490.29791450.20571457X-RAY DIFFRACTION94
1.8949-1.95070.27521350.19561469X-RAY DIFFRACTION95
1.9507-2.01360.24551370.19281488X-RAY DIFFRACTION96
2.0136-2.08560.25481390.19611491X-RAY DIFFRACTION97
2.0856-2.16910.23491440.19731490X-RAY DIFFRACTION97
2.1691-2.26780.24541470.18691514X-RAY DIFFRACTION98
2.2678-2.38740.22271390.20391494X-RAY DIFFRACTION98
2.3874-2.5370.24871520.19811524X-RAY DIFFRACTION98
2.537-2.73280.23991400.20761512X-RAY DIFFRACTION98
2.7328-3.00780.25621460.21391530X-RAY DIFFRACTION98
3.0078-3.44290.2921440.18941517X-RAY DIFFRACTION97
3.4429-4.33730.2061420.17571529X-RAY DIFFRACTION97
4.3373-47.47570.23151430.20611566X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -0.3765 Å / Origin y: 4.6258 Å / Origin z: 13.8105 Å
111213212223313233
T0.1168 Å2-0.0046 Å2-0.0169 Å2-0.1416 Å2-0.0025 Å2--0.1293 Å2
L0.4781 °20.3143 °2-0.3907 °2-0.4326 °2-0.2814 °2--0.6969 °2
S-0.0244 Å °0.0546 Å °-0.0026 Å °0.0184 Å °0.0135 Å °-0.0007 Å °-0.0004 Å °0.0171 Å °-0 Å °
Refinement TLS groupSelection details: all

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