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- PDB-7vd4: Crystal structure of BPTF-BRD with ligand TP248 bound -

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Basic information

Entry
Database: PDB / ID: 7vd4
TitleCrystal structure of BPTF-BRD with ligand TP248 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-6FI / Bromodomain PHD finger transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85659146555 Å
AuthorsLu, T. / Lu, H.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2022
Title: Discovery of a highly potent CECR2 bromodomain inhibitor with 7H-pyrrolo[2,3-d] pyrimidine scaffold.
Authors: Lu, H. / Lu, T. / Zu, S. / Duan, Z. / Guang, Y. / Li, Q. / Ma, J. / Chen, D. / Li, B. / Lu, W. / Jiang, H. / Luo, C. / Ye, D. / Chen, K. / Lin, H.
History
DepositionSep 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 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)13,7512
Polymers13,3861
Non-polymers3641
Water95553
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6720 Å2
Unit cell
Length a, b, c (Å)111.923, 27.219, 38.727
Angle α, β, γ (deg.)90.000, 98.031, 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

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Components

#1: Protein Nucleosome-remodeling factor subunit BPTF


Mass: 13386.286 Da / Num. of mol.: 1
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-6FI / 6-[4-[3-(dimethylamino)propoxy]phenyl]-N-methyl-2-methylsulfonyl-pyrimidin-4-amine


Mass: 364.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24N4O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
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: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. obs: 9679 / % possible obs: 96.37 % / Redundancy: 6 % / CC1/2: 0.897 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.05 / Rrim(I) all: 0.128 / Rsym value: 0.05 / Net I/σ(I): 97.7
Reflection shellResolution: 1.858→1.925 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 840 / CC1/2: 0.89 / Rpim(I) all: 0.209 / Rrim(I) all: 0.512 / Rsym value: 0.209

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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: 1.85659146555→24.1139720626 Å / SU ML: 0.197206659844 / Cross valid method: NONE / σ(F): 1.36344065761 / Phase error: 37.5725600949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24635789781 465 4.81316633889 %
Rwork0.205881942559 9196 -
obs0.208045391853 9661 96.2155163828 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5877722999 Å2
Refinement stepCycle: LAST / Resolution: 1.85659146555→24.1139720626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms915 0 25 53 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00903290312713977
X-RAY DIFFRACTIONf_angle_d0.9612654935611331
X-RAY DIFFRACTIONf_chiral_restr0.0475600790557136
X-RAY DIFFRACTIONf_plane_restr0.00482106183416172
X-RAY DIFFRACTIONf_dihedral_angle_d19.6946764295591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8566-2.12510.3129680059771290.2423127395642921X-RAY DIFFRACTION92.789777913
2.1251-2.67690.3120108531961650.23125604313115X-RAY DIFFRACTION98.5873159002
2.6769-100.2135203309311710.1899098303663160X-RAY DIFFRACTION97.1987160782

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