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- PDB-5ml0: Bromodomain of Mouse PCAF with (R)-4-chloro-2-methyl-5-((1-methyl... -

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Basic information

Entry
Database: PDB / ID: 5ml0
TitleBromodomain of Mouse PCAF with (R)-4-chloro-2-methyl-5-((1-methylpiperidin-3-yl)amino)pyridazin-3(2H)-one
ComponentsHistone acetyltransferase KAT2B
KeywordsTRANSCRIPTION / INHIBITOR / HISTONE / EPIGENETIC READER / BROMODOMAIN / PCAF / ANTAGONIST
Function / homology
Function and homology information


YAP1- and WWTR1 (TAZ)-stimulated gene expression / Formation of WDR5-containing histone-modifying complexes / B-WICH complex positively regulates rRNA expression / Regulation of FOXO transcriptional activity by acetylation / negative regulation of rRNA processing / Metalloprotease DUBs / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / histone H3K9 acetyltransferase activity ...YAP1- and WWTR1 (TAZ)-stimulated gene expression / Formation of WDR5-containing histone-modifying complexes / B-WICH complex positively regulates rRNA expression / Regulation of FOXO transcriptional activity by acetylation / negative regulation of rRNA processing / Metalloprotease DUBs / NOTCH1 Intracellular Domain Regulates Transcription / RUNX3 regulates NOTCH signaling / Notch-HLH transcription pathway / histone H3K9 acetyltransferase activity / diamine N-acetyltransferase / diamine N-acetyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of centriole replication / positive regulation of attachment of mitotic spindle microtubules to kinetochore / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / lysine N-acetyltransferase activity, acting on acetyl phosphate as donor / Estrogen-dependent gene expression / actomyosin / positive regulation of fatty acid biosynthetic process / internal peptidyl-lysine acetylation / negative regulation of cyclin-dependent protein serine/threonine kinase activity / histone H3 acetyltransferase activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / ATAC complex / I band / cellular response to parathyroid hormone stimulus / limb development / A band / SAGA complex / peptide-lysine-N-acetyltransferase activity / regulation of tubulin deacetylation / histone acetyltransferase binding / acetyltransferase activity / regulation of cell division / regulation of RNA splicing / regulation of embryonic development / histone acetyltransferase complex / regulation of DNA repair / positive regulation of lipid biosynthetic process / histone acetyltransferase activity / histone acetyltransferase / positive regulation of gluconeogenesis / positive regulation of glycolytic process / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / mitotic spindle / kinetochore / memory / positive regulation of neuron projection development / histone deacetylase binding / vasodilation / cellular response to insulin stimulus / rhythmic process / heart development / cellular response to oxidative stress / DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / chromatin remodeling / negative regulation of cell population proliferation / centrosome / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A ...PCAF, N-terminal / Histone acetyltransferase GCN5/PCAF / PCAF (P300/CBP-associated factor) N-terminal domain / Histone acetyltransferase GCN5 / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-P2L / Histone acetyltransferase KAT2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsChung, C.-W.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe.
Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. ...Authors: Humphreys, P.G. / Bamborough, P. / Chung, C.W. / Craggs, P.D. / Gordon, L. / Grandi, P. / Hayhow, T.G. / Hussain, J. / Jones, K.L. / Lindon, M. / Michon, A.M. / Renaux, J.F. / Suckling, C.J. / Tough, D.F. / Prinjha, R.K.
History
DepositionDec 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5724
Polymers13,1911
Non-polymers3813
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint5 kcal/mol
Surface area6960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.481, 93.481, 32.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1216-

HOH

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Components

#1: Protein Histone acetyltransferase KAT2B / Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP- ...Histone acetyltransferase PCAF / Histone acetylase PCAF / Lysine acetyltransferase 2B / P300/CBP-associated factor / P/CAF


Mass: 13191.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kat2b, Pcaf / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHD1, histone acetyltransferase
#2: Chemical ChemComp-P2L / 4-chlorol-2-methyl-5-[[(3~{R})-1-methylpiperidin-3-yl]amino]pyridazin-3-one


Mass: 256.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17ClN4O
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% P550MME P20K, 0.1M Morpheus buffer 3 pH8.5, 10% morpheus amino acids

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.64→30.39 Å / Num. obs: 12718 / % possible obs: 97 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.017 / Net I/σ(I): 50.7
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 20.8 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→30.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.737 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22181 622 4.9 %RANDOM
Rwork0.17852 ---
obs0.18064 12089 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å20 Å2
2---0.07 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.64→30.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms913 0 25 220 1158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.019981
X-RAY DIFFRACTIONr_bond_other_d0.0020.02943
X-RAY DIFFRACTIONr_angle_refined_deg1.0121.961319
X-RAY DIFFRACTIONr_angle_other_deg0.77932181
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3265111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54123.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.83815181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.637157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 38 -
Rwork0.253 725 -
obs--79.15 %
Refinement TLS params.Method: refined / Origin x: -3.4236 Å / Origin y: 16.329 Å / Origin z: 2.8655 Å
111213212223313233
T0.0138 Å2-0.0058 Å20.0026 Å2-0.0106 Å20.005 Å2--0.0146 Å2
L1.1643 °2-0.5351 °2-0.1394 °2-0.9499 °2-0.1819 °2--0.1028 °2
S0.0243 Å °0.08 Å °0.0718 Å °0.0015 Å °-0.0448 Å °-0.1143 Å °-0.0055 Å °-0.0076 Å °0.0205 Å °

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