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- PDB-7kpy: Crystal structure of CBP bromodomain liganded with UMB298 (compou... -

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Basic information

Entry
Database: PDB / ID: 7kpy
TitleCrystal structure of CBP bromodomain liganded with UMB298 (compound 23)
ComponentsHistone acetyltransferase
KeywordsTRANSCRIPTION / epigenetics / inhibitor / drug development / multi domain proteins
Function / homology
Function and homology information


histone acetyltransferase complex / histone acetyltransferase activity / histone acetyltransferase / chromatin DNA binding / transcription regulator complex / transcription coactivator activity / nuclear body / positive regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein ...Coactivator CBP, KIX domain / CREB-binding protein/p300, atypical RING domain / CBP/p300-type histone acetyltransferase domain / CBP/p300, atypical RING domain superfamily / KIX domain / CREB-binding protein/p300, atypical RING domain / KIX domain profile. / CBP/p300-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein / Coactivator CBP, KIX domain superfamily / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-WU1 / histone acetyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchonbrunn, E. / Bikowitz, M.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Development of Dimethylisoxazole-Attached Imidazo[1,2- a ]pyridines as Potent and Selective CBP/P300 Inhibitors.
Authors: Muthengi, A. / Wimalasena, V.K. / Yosief, H.O. / Bikowitz, M.J. / Sigua, L.H. / Wang, T. / Li, D. / Gaieb, Z. / Dhawan, G. / Liu, S. / Erickson, J. / Amaro, R.E. / Schonbrunn, E. / Qi, J. / Zhang, W.
History
DepositionNov 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: 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: Histone acetyltransferase
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8407
Polymers27,6962
Non-polymers1,1445
Water3,639202
1
A: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3893
Polymers13,8481
Non-polymers5412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4514
Polymers13,8481
Non-polymers6033
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.880, 34.680, 90.740
Angle α, β, γ (deg.)90.000, 116.246, 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-1396-

HOH

21A-1406-

HOH

31B-1383-

HOH

41B-1396-

HOH

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Components

#1: Protein Histone acetyltransferase


Mass: 13847.882 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CREBBP / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: I3L466, histone acetyltransferase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-WU1 / 2-[2-(3-chloranyl-4-methoxy-phenyl)ethyl]-~{N}-cyclohexyl-7-(3,5-dimethyl-1,2-oxazol-4-yl)imidazo[1,2-a]pyridin-3-amine


Mass: 479.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.7→19.17 Å / Num. obs: 27564 / % possible obs: 98.1 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.103 / Net I/σ(I): 8.7
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 1995 / CC1/2: 0.743 / Rrim(I) all: 0.844 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NR7

4nr7


Resolution: 1.7→19.17 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.8884
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1379 5 %random
Rwork0.2019 26178 --
obs0.2038 27557 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 80 202 2206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722109
X-RAY DIFFRACTIONf_angle_d1.05342870
X-RAY DIFFRACTIONf_chiral_restr0.0576288
X-RAY DIFFRACTIONf_plane_restr0.0072366
X-RAY DIFFRACTIONf_dihedral_angle_d22.3267287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.760.38191360.30282583X-RAY DIFFRACTION97.25
1.76-1.830.31931350.26122558X-RAY DIFFRACTION97.19
1.83-1.910.3471370.24762599X-RAY DIFFRACTION98.49
1.91-2.020.32411360.23372583X-RAY DIFFRACTION98.02
2.02-2.140.27391350.20372566X-RAY DIFFRACTION97.9
2.14-2.310.22981390.20062639X-RAY DIFFRACTION98.69
2.31-2.540.24871380.20282628X-RAY DIFFRACTION99
2.54-2.90.22971390.21142632X-RAY DIFFRACTION99.14
2.9-3.660.19981400.18972654X-RAY DIFFRACTION99.08
3.66-19.170.20981440.17612736X-RAY DIFFRACTION98.7

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