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- PDB-7f5e: Crystal structure of BPTF-BRD with ligand DC-BPi-11 bound -

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Basic information

Entry
Database: PDB / ID: 7f5e
TitleCrystal structure of BPTF-BRD with ligand DC-BPi-11 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-1IY / Bromodomain PHD finger transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20017124371 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)13,7842
Polymers13,3861
Non-polymers3971
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6620 Å2
Unit cell
Length a, b, c (Å)111.448, 27.157, 38.697
Angle α, β, γ (deg.)90.000, 98.534, 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-1IY / N,N-dimethyl-3-[5-(2-methylsulfonyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)indol-1-yl]propan-1-amine


Mass: 397.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N5O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 5770 / % possible obs: 95.39 % / Redundancy: 5.8 % / Biso Wilson estimate: 24.5012967654 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Rrim(I) all: 0.108 / Rsym value: 0.099 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.537 / Num. unique obs: 462 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.162 / Rrim(I) all: 0.385 / Rsym value: 0.537

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Processing

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

3qzt


Resolution: 2.20017124371→29.4517037408 Å / SU ML: 0.306121192389 / Cross valid method: FREE R-VALUE / σ(F): 1.33789259305 / Phase error: 27.5608043314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.272618350664 308 5.33795493934 %
Rwork0.187252262267 5462 -
obs0.191574074786 5770 95.434998346 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.1906488631 Å2
Refinement stepCycle: LAST / Resolution: 2.20017124371→29.4517037408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms904 0 28 52 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864577475891009
X-RAY DIFFRACTIONf_angle_d0.967222754941380
X-RAY DIFFRACTIONf_chiral_restr0.0460925284682139
X-RAY DIFFRACTIONf_plane_restr0.00496230411197176
X-RAY DIFFRACTIONf_dihedral_angle_d18.1705081273622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.77170.3044245445271560.1939344800712557X-RAY DIFFRACTION90.8573342264
2.7717-3.50.2572933221221520.1846461332092905X-RAY DIFFRACTION99.9019607843

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