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- PDB-7f5c: Crystal structure of BPTF-BRD with ligand DC-BPi-07 bound -

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Basic information

Entry
Database: PDB / ID: 7f5c
TitleCrystal structure of BPTF-BRD with ligand DC-BPi-07 bound
ComponentsNucleosome-remodeling factor subunit BPTF
KeywordsANTITUMOR PROTEIN / BPTF Bromodomain / Lysine acetylation / small-molecule inhibitor / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


NURF complex / regulation of transcription by RNA polymerase II / zinc ion binding
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / PHD-finger / 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 ...Nucleosome-remodeling factor subunit BPTF / PHD-finger / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-EUU / Bromodomain PHD finger transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65004485921 Å
AuthorsLu, T. / Lu, H.B. / Wang, J. / Lin, H. / Lu, W. / Luo, C.
CitationJournal: To Be Published
Title: Discovery and Optimization of Small-Molecule Inhibitors for the BPTF Bromodomains Proteins
Authors: Lu, T. / Lu, H.B. / Wang, J. / Han, J. / Xiao, S. / Jiang, H. / Chen, Y. / Yang, F. / Li, Q. / Jiang, H.L. / Chen, K.X. / Lu, W.C. / Lin, H. / Luo, C.
History
DepositionJun 21, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleosome-remodeling factor subunit BPTF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2772
Polymers12,8621
Non-polymers4161
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6590 Å2
Unit cell
Length a, b, c (Å)111.309, 27.148, 38.695
Angle α, β, γ (deg.)90.000, 98.202, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF


Mass: 12861.676 Da / Num. of mol.: 1 / Fragment: Bromodomain PHD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF / Production host: Escherichia coli (E. coli) / References: UniProt: J3QQQ8
#2: Chemical ChemComp-EUU / 6-[1-[3-(dimethylamino)propyl]indol-5-yl]-2-methylsulfonyl-N-propyl-pyrimidin-4-amine


Mass: 415.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 13478 / % possible obs: 95.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.7078791478 Å2 / CC1/2: 0.957 / CC star: 0.989 / Rpim(I) all: 0.129 / Rrim(I) all: 0.317 / Rsym value: 0.072 / Net I/σ(I): 95.5
Reflection shellResolution: 1.65→1.709 Å / Rmerge(I) obs: 0.072 / Num. unique obs: 13479 / CC1/2: 0.958 / CC star: 0.997 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Rsym value: 0.072

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
Aimlessdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QZT

3qzt


Resolution: 1.65004485921→29.5328097045 Å / SU ML: 0.142474931923 / Cross valid method: FREE R-VALUE / σ(F): 1.38114905848 / Phase error: 21.5564449971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.216791998029 684 5.07493693426 %
Rwork0.182867528743 12794 -
obs0.184575034066 13478 95.4127141441 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.2090379212 Å2
Refinement stepCycle: LAST / Resolution: 1.65004485921→29.5328097045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 29 132 1065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005437390271991009
X-RAY DIFFRACTIONf_angle_d0.8877055824341378
X-RAY DIFFRACTIONf_chiral_restr0.0462703971467139
X-RAY DIFFRACTIONf_plane_restr0.00538946196785176
X-RAY DIFFRACTIONf_dihedral_angle_d18.012332252625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.2428266734811170.1839456122532148X-RAY DIFFRACTION81.4162473041
1.7774-1.95630.2250793048671540.1773812366972544X-RAY DIFFRACTION95.6737588652
1.9563-2.23930.1873026850571310.1682212182262661X-RAY DIFFRACTION99.8926654741
2.2393-2.82090.2299993407371230.1832685409542686X-RAY DIFFRACTION100
2.8209-3.55310.2162507385891590.1901799604482755X-RAY DIFFRACTION99.8629198081

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